Whole Genome de novo Assembly
De novo whole genome analysis involves analyzing data from a genome that has been sequenced for the first time, and assembling it without any reference. Assembling typically begins with a series of short sequencing reads that are joined together to form contigs by an assembler. These contigs are joined together to form a scaffold. When analyzing a de novo genome, no map is available to guide the assembly. The four basic steps to assembly include:
1) preprocessing filtering - detecting and correcting erroneous reads before the assembly can begin
2) a graph construction process - organizes short read sequences into a compact form to create longer reads during assembly
3) graph simplification - reduction of graph nodes and edges
4) post processing filtering - contig building and extending contigs into scaffolds
Providers offering Whole Genome de novo Assembly (found 25)
Parseq Lab
CzechiaParseq Lab is experienced in: - massively parallel sequencing data analysis - client-tailored algorithms and software development - analysis pipelines deployment
We offer: - whole genome/exome and targeted sequencing data analysis - de novo assembly - SGV detection and annotation - expression analyses - metagenomics analysis - transcriptomics analysis - proteomics research - genuine task-specific workflows design - custom bioinformatics applications development - statistical data analysis
Collaborations: genomic research labs, sequencing facilities, academic and research institutions.
Years in service: 13Other services offered by Parseq Lab:
| Service | Description | Price |
|---|
Igenbio, Inc.
United States of AmericaExpertise:
Igenbio, Inc. develops genome analysis products and services for the life science industry. Our scientists have broad experience in both in silico and wet lab sequencing, research and development with more than 100 relevant publications in these areas. Igenbio has a proven track record of delivering scientific results for academic, governmental, and industrial institutions for two decades.
Our expertise includes, but is not limited to:
- Whole Genome Sequencing
- RNA-Sequencing
- Metatranscriptomics Sequencing
- Metagenome Sequencing
- Common and custom amplicon sequencing
- Genome Assembly & Annotation
- RNA-Seq Analysis
- Amplicon Sequencing Analysis
- Metagenome Analysis
- Genome ORF calling: Eukaryotes and Prokaryote Genomes
- Pathway Analysis
- Metabolic Reconstruction
- SNP Discovery & Analysis
- Comparative Genomics
- Available for all organisms, including humans, animals, plants, bacteria, and viruses.
- Haploid, diploid or polyploid assemblies
Infrastructure:
Igenbio has a large, secure cloud infrastructure that can expand to meet any project demands you may have - from large number of samples to quick turnaround times. Please inquire for more information.
At Igenbio, Inc. security of your data is a top priority. Your data is protected by best practices in physical and data security measures. This includes 24/7 physical security and monitoring, and the best available encryption for storage and transmission. Our employees are trained and knowledgeable in data security best practices.
Years in service: 11Other services offered by Igenbio, Inc.:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Inquire | |
| Comparative Genome Analysis | Inquire | |
| Metagenomic Analysis | - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 and Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva,… | Inquire |
| SNP / Indel Calling | Inquire | |
| SNP/SV/CNV Discovery | Inquire | |
| Genome Annotation | Gene Annotation and Functional Assignments placing genes into their functional or metabolic context utilizing KEGG Pathways, Gene Ontology, and the ERGO database. Optional - Identification of Antibiotic Resistance - including the genes, pathways, and specific drugs | Inquire |
| Transcriptome de novo Assembly | Inquire | |
| Transcriptome Annotation | Inquire | |
| Transcriptome Annotation | Inquire | |
| Variant Annotation | Inquire | |
| Whole Genome de novo Assembly | All current sequencing technologies support - Illumina, PacBio, Oxford Nanopore, 10x, Hi-C, Ion Torrent, and others. Igenbio scientists utilize a multitude of assembly strategies - denovo, reference based, hybrid, metagenomic, and others. | Inquire |
| Base Calling | Inquire | |
| Microbiome Analysis | - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 or Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva, Gree… | Inquire |
Genotypic Technology
NGS provider IndiaGenotypic Technology is the first genomics company based in India with a state-of-the-art, ISO 9001:2008 accredited, SAP-enabled, 12,000 square feet facility in Bangalore. Our high-throughput facility enables us to offer customized services for experiment design consultation, protocol optimization, microarray and probe designing, next-generation sequencing (NGS), and bioinformatics solutions to clients from academia, biotech, and pharma sectors worldwide.
We have been providing high-quality sequencing services, including whole-genome sequencing (WGS), transcriptome sequencing, shotgun metagenome sequencing, and de-novo assembly since 2000. Our skilled team has experience in working with genomes of all sizes and nucleic acids from various sources on Illumina, Oxford Nanopore, and other platforms. We have developed targeted panels for various viruses like Adenovirus, KFDV, SARS-CoV-2, Dengue, and pipelines for predicting virulent strains that may be difficult to treat with conventional antibiotics.
Our broad range of metagenome services includes targeted and whole-genome metagenome and metatranscriptome sequencing. Our long amplicon metagenome approach provides the best resolution of microbes up to the sub-species level, while whole-genome metagenome sequencing enables the identification of gene clusters, resistome, and novel pathways in a given environment. We also specialize in Ribo-footprinting and RNA immunoprecipitation sequencing, ChIP sequencing, and targeted methylation sequencing.
Years in service: 25Other services offered by Genotypic Technology:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Differential Gene expressions, SNP variants and annotations with known reference, SSR discovery | $69.00 USD (per sample) |
| Transcriptome Mapping | $25.00 USD (per sample) | |
| Custom scripting and special projects | Bioinformatics support for 1 day - includes skype/webex consultation with detailed report. | 120.00 |
| Read Filtering and Cleaning | $2.00 USD (per sample) | |
| Exome Analysis | Exome analysis - from raw data to VCF files and annotations from dbSNP, 1000 genome, COSMIC, SIFT, Polyphen2 and more | $45.00 USD (per sample) |
| ChIP-Seq Analysis | $250.00 USD (per sample) | |
| Metagenomic Analysis | $25.00 USD (per sample) | |
| Transcriptome de novo Assembly | Denovo transcriptome assembly with differential gene expression values. | $600.00 USD (per sample) |
| Whole Genome de novo Assembly | $2900.00 USD (per sample) | |
| Base Calling | $20.00 USD (per hour) |
TACGenomics
United States of AmericaTACGenomics has a team composed of bioinformatician, molecular biologist and computer scientist who are all at Ph.D. level. Our team has the experience of hundreds of NGS data analysis projects from all over the world. The mission of TACGenomics is to help our customer to solve the biological questions. After computation analysis completed by the bioinformatician, our molecular biologist will interpret the analyzed data carefully, provide more insight into your project and help the publication of the project in the high impact journal.
Years in service: 9Other services offered by TACGenomics:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was used to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis. | $50.00 USD (per sample) |
| Transcriptome Mapping | The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. TMM (trimmed mean of M-values) was used to normalize the gene expression. | $50.00 USD (per sample) |
| Custom scripting and special projects | $50.00 USD (per hour) | |
| Exome Analysis | Our team has successfully discovered a causal variant which lead to a mendelian disorder through analyzing 20 samples in three-generation family. The error rate of genotype we called in this family is only 0.2% which indicate that our pipeline detect all the SNV very accurately. | $80.00 USD (per sample) |
| ChIP-Seq Analysis | $80.00 USD (per sample) | |
| Genome Mapping | $50.00 USD (per sample) | |
| Metagenomic Analysis | $100.00 USD (per sample) | |
| Methylation Analysis | $100.00 USD (per sample) | |
| Transcriptome de novo Assembly | $100.00 USD (per sample) | |
| Whole Genome de novo Assembly | $1000.00 USD (per sample) | |
| Microbiome Analysis | $50.00 USD (per sample) |
Biosof LLC
United States of AmericaExpertise:
Expertise in mainly with plant genomes (wheat, tomato, potato, tobacco, rice, maize, diatoms and arabidopsis).
Infrastructure:
Access to over 800 cores (2.3Ghz and faster) SMP compute cluster. Access to over 50TB of raw storage. Computing infrastructure includes all commonly used bioinformatics software and databases. All computing infrastructure is maintained by a 24/7 IT service.
Other services offered by Biosof LLC:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Inquire | |
| Comparative Genome Analysis | Inquire | |
| Custom scripting and special projects | Inquire | |
| Read Filtering and Cleaning | Inquire | |
| SNP / Indel Mapping | Inquire | |
| Genome Mapping | Inquire | |
| SNP / Indel Calling | Inquire | |
| SNP/SV/CNV Discovery | Inquire | |
| Genome Annotation | Inquire | |
| Transcriptome de novo Assembly | Inquire | |
| Transcriptome Annotation | Inquire | |
| Variant Annotation | Inquire | |
| Whole Genome de novo Assembly | Inquire |
Gringene Bioinformatics
New ZealandGringene Bioinformatics provides workflow optimisation services for research that involves the use of computers, enabling researchers to carry out their research faster, cheaper, and better. It is frequently the case that a repetitive task using computers can be sped up 5-10 times by the application of computing methods that are more appropriate to the task at hand.
Gringene Bioinformatics has particular skills in the following areas:
- Theoretical Genetics
- Next-Generation Sequencing
- Computational scripting
- Large-scale data analysis
- Program language translation (porting)
- Debugging / bug reporting
Expertise:
- Homo sapiens (genome mapping, methylation analysis, SNP analysis, STR analysis, population clustering, haplotype analysis, differential expression analysis)
- Environmental samples (16s rRNA mapping, large-scale BLAST analysis, taxonomy analysis)
- Schmidtea mediterranea (transcriptome assembly, genome mapping, transcriptome mapping, differential expression analysis)
- Saccharomyces cerevisiae (codon analysis, gradient peak analysis, genome mapping, transcriptome mapping)
- Drosophila melanogaster (quantitative phenotyping, differential expression analysis)
- Neisseria meningitidis (genome mapping, differential expression analysis)
Infrastructure:
Main processing workstation: 12-thread Intel "desktop" with 64GB memory and 3TB hard drive space (expandable as necessary). I encourage clients to purchase their own bioinformatics servers / workstations, and will use remote systems for analysis when available.
Other services offered by Gringene Bioinformatics:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Inquire | |
| Transcriptome Mapping | Inquire | |
| Custom scripting and special projects | Inquire | |
| Other Services | Inquire | |
| Genome Mapping | Inquire | |
| Transcriptome de novo Assembly | Inquire | |
| Whole Genome de novo Assembly | Inquire |
ContigExpress, LLC
United States of AmericaContigExpress is the leading integrated genomics data service provider. We offer genomic project management, data analysis, and bio-IT consulting services. Our unique value to our clients lies in our deep understanding of both biology and informatics. From project consultation, bio-IT infrastructure implementation, to data analysis, our experienced scientists deliver not only cost-effective customized informatic solutions but also their expert insights.
Our team consists of Ph.D.-level computational biologists with extensive training and professional practice in bioinformatics and genomic research. We understand both your cutting-edge research and your informatics challenges. We enable you and your team to extract actionable information from the vast amount of genomic data in a cost-effective and timely fashion.
We at ContigExpress strive to deliver affordable expert genomic data solutions to researchers and clinicians. We place the utmost emphasis on information confidentiality, data security, and data integrity. Please schedule a complimentary project discussion with one of our expert bioinformaticians to discover how we can help you move your genomics research forward!
Years in service: 14Other services offered by ContigExpress, LLC:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Following is a list of common analysis items for RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Gene and transcript-based quantitation, RPKM/FPKM-based quantitation, Raw hit count-based … | Inquire |
| Other Services | We are a professional bioinformatics service provider and we are happy to provide customized informatic solutions to your unique research and business needs. Please feel free to reach out to us to discuss how we can help you. | Inquire |
| Exome Analysis | Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP… | Inquire |
| ChIP-Seq Analysis | Following is a list of common analysis items for ChIP-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Peaking calling with or without control samples 5) Gene assignment and peak annotation 6)… | Inquire |
| Small RNA Mapping | Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known micr… | Inquire |
| Genome Mapping | Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel char… | Inquire |
| Metagenomic Analysis | Following is a list of common analysis items for Metagenomics Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Sequence assembly 4) Biodiversity analysis and binning 5) Gene predication and functional annotation 6) Gene Ontology and path… | Inquire |
| SNP/SV/CNV Discovery | Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel char… | Inquire |
| Targeted Capture Analysis | Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP… | Inquire |
| Genome Annotation | Following is a list of common analysis items for Genome Annotation. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Gene prediction with or without RNASeq data 3) BLAST-based gene function annotation 4) Written project report with analysis methods, publication-ready graph… | Inquire |
| Small RNA Annotation | Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known micr… | Inquire |
| Methylation Analysis | Following is a list of common analysis items for Methylation Sequencing, including MeDIP-Seq, hMeDIP-Seq, RRBS / Targeted Bisulfite-Seq, WGBS, and 5-mc RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Methylation state-sensitive mapping 4) … | Inquire |
| Transcriptome de novo Assembly | Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Transcriptome assembly, scaffolding and gap closure 4) Gene annotation (molecular function, Gene Ontology and pathways) 5) SNP disc… | Inquire |
| Transcriptome Annotation | Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Project consultation 2) Transcriptome annotation (molecular functions, Gene Ontology and pathway) 3) Written project report with analysis methods, publication-ready graphics, and references | Inquire |
| Whole Genome de novo Assembly | Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Contig assembly 4) Scaffolding and gap closure 5) Gene/ORF prediction 6) Gene annotation and classification via database search and… | Inquire |
STAB VIDA
NGS provider PortugalOther services offered by STAB VIDA:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Deliverables include the raw data fastq seq files, transcriptome mapping, gene expression analysis and a report (including Q score, number of reads, coverage, etc) | $200.00 USD (per sample) |
| SNP / Indel Mapping | Deliverables include the raw data fastq seq files, consensus sequence, list of genetic variants and a report (including Q score, number of reads, coverage, etc) | $200.00 USD (per sample) |
| Genome Mapping | Deliverables include the raw data fastq seq files, consensus sequence and a report (including Q score, number of reads, coverage, etc) | $200.00 USD (per sample) |
| Whole Genome de novo Assembly | Deliverables include the raw data fastq seq files, list of contigs and a report with results (including Q score, number of reads, coverage etc) | $200.00 USD (per sample) |
| Base Calling | Deliverables include the raw data fastq seq files | Inquire |
Computomics
GermanyBioinformatics Services for Plant Scientists and Breeders by Computomics
At Computomics.com, we deliver in-depth NGS analyses. We start by identifying your breeding or research goals, devise a sequencing strategy to achieve them and define the project deliverables and timeline through an initial consultation. Our methods include the latest algorithms from the bioinformatics community.
We protect the security of your data. We use high-performance servers in a high-security data center with two-factor access control mechanisms. During the analysis, we use transparent, reliable processes and quickly deliver highly reproducible results in constant feedback with you, via virtual or onsite meetings at your location.
Our NGS products are exclusively focusing on plant species and their interacting microbes, and include:
- Reference genome assembly: experience with polyploids and genomes up to 22 Gbp
- Genome annotation: ab initio gene and transcript isoform prediction, protein function, ncRNA annotation
- Genomic variance analysis and comparison: for marker development, phylogenetic studies, and comparative genomics
- Bulk segregation analysis, genotyping, marker development
- Differential gene expression, de novo transcriptome assembly
- World’s fastest, most accurate metagenomics
- Statistically sound epigenetics
- Genomic selection with continuous model improvement
Computomics collaborates with world-leading scientists, opening up an unprecedented opportunity for breeders and plant scientists. We provide data of the highest possible quality that expedite your crop improvement programs.
Years in service: 11Other services offered by Computomics:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Gene expression studies, or RNAseq allow you to sequence the entire transcriptome of a plant, and provide valuable applications in crop improvement programs We and our collaborators have published peer reviewed methods for accurate gene expression analysis. Our RNAseq analyses can determine exact gene expression levels including splice variants. Using machine learning techniques, we identify dif… | Inquire |
| Comparative Genome Analysis | We excel at managing complex crop genomic variance studies. Our analysis can help you obtain a set of genomic markers to enhance rational and controlled breeding procedures. Markers may include single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy number variations (CNVs) or structural variants (SVs). Taking into account the properties of your plant of interest and the … | Inquire |
| Other Services | Bioinformatics Consulting In addition to our next-generation sequencing (NGS) products and services, We also offer individual consulting services. With a team of scientists and partners who are thought leaders in crop genomics, we give impartial advice, independent of any sequencing platform, technology or tool suite. Each consultation is unique, please contact us to receive a quote for your sp… | Inquire |
| Other Services | Introgression and Insertion Delineation Next-generation sequencing is a great tool for molecular characterisation of seeds with genetic modifications or introgressions. We can provide answers to many regulatory and safety related questions, such as: At how many sites was the DNA integrated into the plant genome? What is the exact sequence of each insert? Is the sequence rearranged with respect t… | Inquire |
| Other Services | Genomic Selection with Continuous Model Improvement Genomic Selection with Continuous Model Improvement Genomic selection is a highly successful strategy to predict breeding values in plants. Advances in sequencing and high-throughput variant discovery enable the collection of tens of thousands of markers for hundreds of plants, providing exciting opportunities for unleashing the full power of g… | Inquire |
| Read Filtering and Cleaning | Inquire | |
| Metagenomic Analysis | World’s Fastest, Most Accurate Metagenomics Plants interacts constantly with soil-borne microbes. These interactions vary from symbiotic to pathogenic. In a metagenomics study of the rhizosphere, DNA or RNA are sequenced using next generation sequencing instruments. Sequences that do not originate from the plant host are analysed to identify genes and species contained within the sample. A tax… | Inquire |
| Genome Annotation | We perform de novo genome annotation using the latest in silico predictive approaches and RNAseq reads. We offer two machine learning-based gene prediction methods that can be trained to recognise biological features in your crop’s genome. The resources we use to build an annotation map include existing annotations for related organisms, RNAseq data, and PacBio complete isoforms. We use all avai… | Inquire |
| Methylation Analysis | Statistically Sound Epigenetics Non-genetic factors affect crops traits and phenotypes. Identifying epigenetic patterns allow breeders and plant scientists to uncover expression correlations and non-genetically inherited gene regulation patterns. We specialize in crop epigenetics. Methylation of cytosine residues is a known mechanism for gene silencing and gene expression regulation. We use bi… | Inquire |
| Whole Genome de novo Assembly | We have a deep understanding of both de novo and reference-based genome assembly of large crop genomes. It is crucial to first develop an effective strategy before selecting the appropriate sequencing technology and bioinformatics tools. A de novo genome assembly project must address sources of error up front, like sequence bias and read quality. A crucial point is quality control. We compare o… | Inquire |
Girihlet Inc.
NGS provider United States of AmericaWe specialize in esoteric parts of the genome offering services (sample prep, sequencing and analyses) in areas such as 1) mitochondrial DNA sequencing, 2) TCR repertoire sequencing and 3) small RNA sequencing.
We also perform routine services such as 4) mRNA-seq and 5) whole-exome sequencing. We have prepared samples from mouse, human, drosophila, as well as organisms such as zebrafish and Bats. We have developed novel, custom analytical pipelines for data analysis from each species.
Years in service: 9Other services offered by Girihlet Inc.:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | 1. Gene-level expression estimation (NCBI RefSeq gene set) with annotation for each sample. 2. Transcript-level expression estimation (NCBI RefSeq transcript set) with annotation for each sample. 3. Gene-level differential expression assessment with annotation for one pairwise comparison. 4. Transcript-level differential expression assessment with annotation for one pairwise comparison. 5. En… | $225.00 USD (per sample) |
| Small RNA Mapping | mapping and differential expression assessment with annotation for one pairwise comparison. | $225.00 USD (per sample) |
| SNP / Indel Calling | novel custom made pipelines (published) to call SNPs and INDEL effectively. | $225.00 USD (per sample) |
| Whole Genome de novo Assembly | $350.00 USD (per sample) |
Labindia-GPOD
IndiaWe provide NGS data analysis services using public domain tools as well as CLC bio workbenches. Our services include primary, secondary and tertiary data analysis of NGs data from all platforms. Data analysis steps include read QC check, Assembly and metrics, Annotation, Variant detection, and annotation and biological interpretations. We also enter in to joint projects as industry partners.
Years in service: 14Other services offered by Labindia-GPOD:
| Service | Description | Price |
|---|---|---|
| Exome Analysis | Exome analysis at our facility is performed using CLC bio Cancer workbench which helps in find and annotate variants more accurately. | $200.00 USD (per sample) |
| Genome Mapping | We perform reference genome mapping using CLC bio Genomic recent version and also available public domain tools to benchmark the results. CLc bio has currently released faster genome mapper. We perform post assembly metrics to check correctness of reference assembly. | $150.00 USD (per sample) |
| Genome Annotation | We perform Genome annotation using BLAST and BLAST2Go tools. We have FPGA based local facility which speeds up the BLAST process | $500.00 USD (per sample) |
| Transcriptome de novo Assembly | Transcriptome de novo assembly and read map back is performed using CLC bio genomic workbench and other public domain tools. This analysis is followed by transcriptome annotation and tertiary analysis like pathaway findings. | $500.00 USD (per sample) |
| Variant Annotation | Variant annotation is performed using CLC bio Cancer Research Workbench. | $600.00 USD (per sample) |
| Whole Genome de novo Assembly | WGS de novo assembly is performed using latest version of the CLC bio Genomic Workbench and available public domain tools. End analysis helps to benchmark the results and robustness of the assembly. Post assembly metrics are performed to check the quality of the assembly | $500.00 USD (per sample) |
UCLA Technology Center for Genomics & Bioinformatics (TCGB)
NGS provider United States of AmericaUCLA Technology Center for Genomics & Bioinformatics (UCLA TCGB) (http://pathology.ucla.edu/tcgb), directed by Dr. Xinmin Li, has 9 Ph.D. level scientists and a total staff of 12, who together have 76 years combined genomics experience. This high throughput genomic Center equipped with all major next generation sequencing instruments, sophisticated bioinformatics tools and big data management systems . The TCGB has Miseq, Nextse, Hiseq, Novaseq, GridION, 10x single cell Chromium system, 10X connect system, Nanostring GeoMx DSP system, automated NGS library construction system, which allow us offering comprehensive services including WGS, WES, RNAseq, Chipseq, Methyseq, 10X single cell sequencings, GeoMx DSP spatial transcriptome sequencing and so on. The TCGB provides these services in a cost-effective and timely manner with guaranteed quality.
Years in service: 17Other services offered by UCLA Technology Center for Genomics & Bioinformatics (TCGB):
| Service | Description | Price |
|---|---|---|
| Other Services | NGS Data Analysis | $223.45 USD (per sample) |
| Other Services | 10X Single Cell Data Analysis | $378.96 USD (per sample) |
| Other Services | 10X Cell Counting & Viability Analysis | $139.23 USD (per sample) |
| Whole Genome de novo Assembly | $233.49 USD (per sample) |
HybridStat Predictive Analytics
GreeceHybridStat is a company bringing together a team of highly qualified and motivated scientists and developers, whose expertise spans a variety of statistics and computer science domains. Main HybridStat’s services are centered on bioinformatics, biostatistics and analytics of high-throughput data derived from modern biological technologies such as Next Generation Sequencing (NGS), DNA microarrays and Mass Spectrometry. In addition, HybridStat offers customized software solutions regarding the above.
Regarding NGS, HybridStat offers a variety of one-stop shop data analysis and analytics services, spanning from genome alignments and preprocessing of raw short read fragments, up to analytical and specialized reports and figures describing the results of various NGS protocols including RNA-Seq (quality control, differential expression and splicing analysis, biochemical pathway enrichments etc.), ChIP-Seq (data normalization and peak calling, gene-binding site associations, methylation profiles, motif finding etc.), Whole Exome and Whole Genome Sequencing (data preprocessing, variant calling, filtering, annotation and interpretation, etc.) and Single Cell Sequencing data analysis, using both open source and optimized proprietary pipelines.
HybridStat, can also offer complete support to your organization through its advanced Whole Exome Sequencing analytics platform Clingon (www.clingon-mds.com). Clingon is a complete, integrated one-stop clinical genomics and medical decision support platform which performs data analysis from raw data up to the generation of clinical reports. It uniquely integrates and curates a handful of resources regarding gene-disease and gene product-drug associations as well as curated variant annotation data towards more timely and accurate results and the optimal design of personalized treatment plans.
Years in service: 10Other services offered by HybridStat Predictive Analytics:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | A fully descriptive and interactive report is provided. | $300.00 USD (flat price) |
| Comparative Genome Analysis | $60.00 USD (per hour) | |
| Custom scripting and special projects | $70.00 USD (per hour) | |
| Other Services | $70.00 USD (per hour) | |
| Read Filtering and Cleaning | $25.00 USD (per sample) | |
| Read Filtering and Cleaning | $30.00 USD (per sample) | |
| Read Filtering and Cleaning | $20.00 USD (per sample) | |
| Exome Analysis | Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. | $150.00 USD (per sample) |
| Exome Analysis | Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. | $170.00 USD (per sample) |
| Exome Analysis | Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. | $200.00 USD (per sample) |
| ChIP-Seq Analysis | ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. | $70.00 USD (per sample) |
| ChIP-Seq Analysis | ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. | $85.00 USD (per sample) |
| ChIP-Seq Analysis | ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. | $100.00 USD (per sample) |
| SNP / Indel Mapping | $30.00 USD (per sample) | |
| SNP / Indel Mapping | $25.00 USD (per sample) | |
| SNP / Indel Mapping | $40.00 USD (per sample) | |
| Genome Mapping | $25.00 USD (per sample) | |
| Genome Mapping | $20.00 USD (per sample) | |
| Genome Mapping | $30.00 USD (per sample) | |
| SNP / Indel Calling | $40.00 USD (per sample) | |
| SNP / Indel Calling | $45.00 USD (per sample) | |
| SNP / Indel Calling | $50.00 USD (per sample) | |
| Variant Annotation | Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. | $40.00 USD (per sample) |
| Variant Annotation | Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. | $50.00 USD (per sample) |
| Variant Annotation | Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. | $60.00 USD (per sample) |
| Whole Genome de novo Assembly | $1000.00 USD (flat price) |
Omega Bioservices
NGS provider United States of AmericaOur facility is unique because we offer the full range of NGS service from sample extraction through to data analysis. Sample extraction capabilities and expertise cover the entire spectrum of both environmental and clinical sample types.
Years in service: 11Other services offered by Omega Bioservices:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. | $110.00 USD (per sample) |
| Differential Gene Expression Analysis | Identify differentially expressed genes among samples using RNA-seq technique. Human, mouse, rat, fruit fly, cattle, pig, chicken, zebrafish, C. elegans, maize, thale cress, Japonica rice (Oryza sativa) and yeast, up to 7.5gb/sample. | $56.00 USD (per sample) |
| Transcriptome Mapping | Map mRNAs to either the reference or the assembled genome. | $332.00 USD (per sample) |
| Custom scripting and special projects | We provide study specific bioinformatics analysis (known as tertiary analysis). such as (not limited to) 1) process secondary sequencing data analysis for a variety of platforms such as Nanostring, Nanopore, single cell expression. 2) integrative analysis across sequencing platforms (such as DNA-seq, RNA-seq, Chip-seq) 3) integrate meta/clinical information, perform association study and build p… | $60.00 USD (per hour) |
| Read Filtering and Cleaning | Examination of sequencing quality and removal of low quality reads prior to downstream analysis provided free of charge with sequencing service if desired. | $110.00 USD (per sample) |
| Exome Analysis | Whole exome sequencing involves capturing the coding region of the genome, or exons (EXpressed regiONS). SNVs and indels are the most important and abundant types of variation in exons. Human exome analysis provided free of charge with sequencing service. | $332.00 USD (per sample) |
| ChIP-Seq Analysis | ChIP-Seq is a technique to identify DNA loci bound by a specific protein. The standard output of ChIP-seq analysis includes peak call and motif enrichment at binidng sites. | $332.00 USD (per sample) |
| Small RNA Mapping | Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. | $221.00 USD (per sample) |
| SNP / Indel Mapping | Mapped to the reference genome and annotated using public database. Analysis for human, mouse, and rat provided free of charge with sequencing service. | $332.00 USD (per sample) |
| Genome Mapping | Genome mapping is a technique used to assign the location of a particular gene on a chromosome and measure their relative locations and distances between genes. Mapping to many model organisms provided free of charge with sequencing service. | $110.00 USD (per sample) |
| Metagenomic Analysis | Metagenomic analysis involves the identification and quantification of genetic material from environmental, uncultured microorganisms. Analysis involving only 16S rRNA amplicon sequences are provided free of charge with sequencing service. | $551.00 USD (per sample) |
| SNP / Indel Calling | Identify SNPs and Indels in the region of interested, using DNA sequencing. Analysis for human, mouse, and rat provided free of charge with sequencing service. | $332.00 USD (per sample) |
| SNP/SV/CNV Discovery | Variants discovery. Analysis for human, mouse, and rat provided free of charge with sequencing service. | $332.00 USD (per sample) |
| Targeted Capture Analysis | Variant call, gene annotation. Provided free of charge with sequencing service. | $332.00 USD (per sample) |
| Genome Annotation | Annotation is the process by which pertinent information about these raw DNA sequences is added to the genome databases. This involves describing different regions of the sequence and identifying which regions can be called genes. | $221.00 USD (per sample) |
| Small RNA Annotation | Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. | $332.00 USD (per sample) |
| Methylation Analysis | The processing of bisulfite sequencing data includes sequence alignment and the quantification of absolute DNA methylation at base resolution. Methylation analysis for data generated from the Illumina TruSeq kit are provided free of charge with sequencing service. | $553.00 USD (per sample) |
| Transcriptome de novo Assembly | Identify and quantify putative mRNA transcripts using RNA-seq data for unannotated species. | $553.00 USD (per sample) |
| Transcriptome Annotation | Annotate or predict functions of transcribed genes using well know gene ontology tools. | $332.00 USD (per sample) |
| Variant Annotation | Identified variants will be mapped to the reference genome and annotated using public database. Analysis for human sequences provided free of charge with sequencing service. | $332.00 USD (per sample) |
| Whole Genome de novo Assembly | Prices vary according to genome type. Please contact our Science Project Team. Some small genome assembly provided free of charge with sequencing service. | $3315.00 USD (per sample) |
| Base Calling | Demultiplex data and convert BCL files to FASTQ files | $110.00 USD (per sample) |
Applied Biological Materials Inc.
NGS provider CanadaCommitted to making newer technologies attainable to modern researchers, abm offers a wide range of sequencing services on the advanced Illumina® sequencing platforms at accessible prices and rapid turnaround times. abm's premium NGS services will not only save valuable time and money, but also provide the most reliable and comprehensive solution for the project's needs.
Advantages of using our NGS services: -dedicated NGS specialists to help with experimental design and data analysis -customizable bioinformatics analysis to suit your project needs -strict quality control at multiple steps in library preparation and sequencing -RNA-seq, miRNA-seq, WGS, metagenomics, Amplicon-Seq and more!
What types of bioinformatics analysis will be done? If the reference genome is available (i.e. human or mouse), read mapping and alignment to the reference genome is included in the service. -Data is available in industry standard formats: FASTQ (default), SFF or BAM. Other formats available upon request (additional fees may apply). -RNA-seq includes: Read mapping and gene expression level estimation
Our data report files are provided in formats that can be viewed with any standard text viewers.
Years in service: 10Other services offered by Applied Biological Materials Inc.:
| Service | Description | Price |
|---|
Minnesota Informatics
United States of AmericaMinnesota Informatics specializes in the analysis of genomic and expression data for reference and non-reference species. We are experienced in the QC, mapping/assembly, quantification and evaluation of NGS data for RNA-Seq, SNP and Single Cell sequencing projects. We have worked with human and model mammal organisms as well as plant and bacterial genomes.
We distill the large NGS datasets down to manageble tables and graphics of significant, differentially expressed or variant genes/loci.
Years in service: 13Other services offered by Minnesota Informatics:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Identify significant genes for RNA-seq or expression data. May be included with mapping projects and price will vary with project size. | Inquire |
| Transcriptome Mapping | Inquire | |
| Read Filtering and Cleaning | QC analysis, trimming and low quality masking/removal. | Inquire |
| ChIP-Seq Analysis | Inquire | |
| SNP / Indel Calling | Identify and qualify SNPs based on transcriptome or regions of interest. Pricing negotiable by project or by the sample. | Inquire |
| SNP/SV/CNV Discovery | Inquire | |
| Transcriptome de novo Assembly | Inquire | |
| Transcriptome Annotation | Inquire | |
| Whole Genome de novo Assembly | Bid will vary with type and size of genome. | Inquire |
Bioinformatics Unit, Panacea Biosciences
NGS provider IndiaOther services offered by Bioinformatics Unit, Panacea Biosciences:
| Service | Description | Price |
|---|---|---|
| Read Filtering and Cleaning | $40.00 USD (per sample) | |
| Exome Analysis | End to End Exome-Seq Data Analysis | $75.00 USD (per sample) |
| ChIP-Seq Analysis | we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. | $80.00 USD (per sample) |
| Genome Mapping | Available only for Human, Mouse and available sequenced geneomes | $75.00 USD (per sample) |
| SNP/SV/CNV Discovery | End to End variant analysis | $70.00 USD (per sample) |
| Small RNA Annotation | Available only for Human, Mouse and available sequenced geneomes | $60.00 USD (per sample) |
| Base Calling | Base calling is the process of assigning bases (nucleobases) to chromatogram peaks. One computer program for accomplishing this job is Phred base-calling, which is a widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. | $50.00 USD (per sample) |
CD Genomics
NGS provider United States of AmericaWe specialize in the services of DNA sequencing, genotyping, DNA library construction and aptamer development. Shotgun Library Sequencing, cDNA Library Sequencing, SAGE Library Sequencing, Whole Genome Sequencing and Primer Walking Sequencing. we offer high quality Re-sequencing & SNP Discovery Services. Quite a few of our staff scientists once participated in the International HapMap Project too.
extensive experience in whole genome shotgun sequencing services. Beginning from bacterial cells or genomic DNA, we provide you with accurate genome consensus sequences. We are also experienced in genome annotation and comparative genomics research. Notably our staff scientists have finished a number of whole microbial genome sequencing projects, such as the genomes of Pseudomonas bathycetes, Bacillus thuringiensis, Thermoanaerobacter tengcongensis, Streptococcus suis, and quite a few virus genomes. In addition, our in-house Laboratory Information Management System (LIMS) as well as manual basecalling ensures the highest service quality.
CD Genomics has been offering professional DNA library construction services for over 5 years. Hundreds of various cDNA libraries (such as standard cDNA library, large insert cDNA library, normalized cDNA library and subtracted cDNA library) and genomic DNA libraries (including short-insert plasmid shotgun library, large-insert plasmid shotgun library, whole genome shotgun library, Fosmid library, Cosmid library, MiniBAC and BAC library) have been constructed in our lab
CD Genomics has been dedicated to provide a full range of services to develop high quality customized aptamers for research, diagnostic and therapeutic applications. Services offered by CD Genomics include aptamer synthesis, aptamer generation, cell aptamer selection, aptamer design and modification, negative selection and so on.
Years in service: 19Other services offered by CD Genomics:
| Service | Description | Price |
|---|---|---|
| Other Services | We provide statistical and bioinformatic data analysis services that help explain the large amounts of data commonly generated by next generation sequencing and genotyping experiments. Our bioinformatic staff consists of all PhD-level scientists trained in bioinformatics, biology and statistics. The software infrastructure for analysis is a combination of custom-built and open-source software. O… | Inquire |
| SNP / Indel Mapping | CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost. Advantages of SNP Microarray Custom, flexible, and scalable; High call rates (> 99%) and high accuracy; Cost-… | $80.00 USD (per sample) |
| Metagenomic Analysis | Key Features and Advantages Longest average read lengths, with~50% of reads longer than 50kb, which exceeds the size of repetitive elements in the average bacterial genome. No DNA amplification. Highest consensus accuracy, low sequencing-context bias Novel bioinformatics analysis programs and pipelines Well-experienced personnel Sample Requirements: gDNA≥5 ug Sequencing Strategy: PacBio Platfo… | 120.00 |
Leucine Rich Bio
IndiaLeveraging the expanding prospects of microbiome research, Leucine Rich Bion has integrated a robust computational pipeline "MetaRich" into a user-friendlyplatform for comprehensive analyses of any microbiome data.
After rigorous testing & validation of several leading microbiome analysis pipelines, tools & databases, we have compiled “MetaRich” to analyze both 16s rDNA & shotgun metagenomes, duly supplemented by our in-house computational tools. MetaRich will assist both researchers & industry personnel who are in pursuit of discovering biological insights within complex microbial systems & will ease the arduous task of large-scale microbiome data analysis.
Years in service: 9Other services offered by Leucine Rich Bio:
| Service | Description | Price |
|---|---|---|
| Microbiome Analysis | For Individual Samples Abundance data - Raw & % Normalized Abundance Bar plots - Raw & % Normalized Pie charts - Kingdom through Phylum Alpha diversity Plots & index value table AMR Prediction Comparative Analyses Differential abundance data (across groups) Abundance Bar plots Raw & % Normalized Alpha diversity Plots & index value table Beta diversity Plots & index value table PCoA analysis & pl… | $9.00 USD (per sample) |
Dreamgenics
NGS provider SpainDreamgenics is a biotech company that offers bioinformatics analysis services for genomic, transcriptomic and metagenomic NGS data using our Genome One software. Genome One (CE-IVD certified) is an advanced tool that allows the integration of all the bioinformatics solutions required for the study, including read alignment, variant calling and annotation. Our analyses identify high-quality genomic variants through high sensitivity and specificity standards, extracting important biological information and reducing validation costs. The services that we offer are the following: WGS, WES, Gene panels, Transcriptomics (RNA-Seq) and Metagenomics. Additionally, we hand in the results using our web viewer Genome One Reports (https://www.dreamgenics.com/en/genome-one/).
The use of our bioinformatics tools allows us to offer you high-quality results in a fast and simple way. By using our analysis services, you considerably reduce costs and the investment in technological devices, informatics and qualified professionals.
Lastly, we are an ISO 9001:2015, UNE-EN ISO 13485:2018 and UNE-ISO/IEC 27001:2017 certified company which represents our commitment to provide our customers with products and services that meet the most demanding quality standards.
Years in service: 12Other services offered by Dreamgenics:
| Service | Description | Price |
|---|---|---|
| Single Cell RNA-Seq Analysis | We offer Single cell RNA-Seq bioinformatic analysis from FASTQ files including: - Sequencing and mapping quality control. - Alignment of reads against reference genome. - Quantification of gene expression at the single cell level. - Reduction of data dimensionality. - Clustering or division of cells into different groups and subgroups. - Differential gene expression analysis. - Study of the evol… | $200.00 USD (per sample) |
| Differential Gene Expression Analysis | Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… | $90.00 USD (per sample) |
| Exome Analysis | Our bioinformatics analysis includes: Quality control, Alignment, Detection of high quality variants (SNVs, translocations and CNVs), Filtering of common variants, Annotation of variants obtained with multiple databases and prediction algorithms and Comparison between samples and extraction of recurrent variants. We will deliver the results to the Genohub data bucket as well as through our platf… | $80.00 USD (per sample) |
| Transcriptome Annotation | Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… | $90.00 USD (per sample) |
DNA Link Inc.
NGS provider United States of AmericaDNA Link was founded in 2000. In the beginning, we offered genome analysis for Universities and Government Institutes supporting a lot of joint research projects. Later we became involved in larger research projects funded by the government and expanded our market to all research, Biotech, Pharmaceutical, foreign institutes and companies. Based on our 20 year-experiences, DNA Link provides options and services in Next generation sequencing, Genotyping, Microarray, Forensics and also personal genomics. Our expertise in research on SNP discovery has lead DNA Link to develop novel personal identification systems called AccuID. DNALink USA, Inc, is based in Los Angeles, CA
Years in service: 24Other services offered by DNA Link Inc.:
| Service | Description | Price |
|---|---|---|
| Transcriptome Mapping | 1. Basic bioinformatics analysis Sequencing Summary Alignment Summary Summarizing plots o Density plot, Box plot, GSEA, Scatter plot, Volcano plot List of genes expressed differentially between given classes List of transcripts expressed differentially between given classes Pathway analysis using DAVID 2. Advanced bioinformatics analysis (optional) Fusion gene analysi… | Inquire |
| Exome Analysis | 1. Basic bioinformatics analysis: Analysis using GATK(2.7) best practices guideline Sequencing Summary Alignment Summary Depth Coverage Plot Genotype Calling and SNP detection Germline & Somatic Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP4500 2.… | Inquire |
| ChIP-Seq Analysis | 1. Basic bioinformatics analysis Sequencing Summary Alignment Summary List of peak positions identified by ChIP-seq tools Input data is transformed into applicable bam or wig format, as needed for visualization by commonly used genome browsers (e.g. IGV or UCSC Genome Browser) 2. Advanced bioinformatics analysis (optional) Medip Peak analyzer Customized Analysis(Client… | Inquire |
| Small RNA Mapping | 1. Basic bioinformatics analysis Sequencing Summary Alignment Summary Visualization plot o Density plot, Box plot, GSEA, Scatter plot, Volcano plot 2. Advanced bioinformatics analysis (optional) Target scan Analysis (limited to specific species) Pathway Analysis Customized Analysis(Client Support) | Inquire |
| Genome Mapping | 1. Basic bioinformatics analysis Analysis using GATK(2.7) best practices guideline Sequencing Summary Alignment Summary Depth Coverage Plot Genotype Calling and SNP detection Germline & Somatic Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP450… | Inquire |
| Targeted Capture Analysis | Analysis using GATK(2.7) best practices guideline Sequencing Summary Alignment Summary Depth Coverage Plot Genotype Calling and SNP detection Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP4500 2. Advanced bioinformatics analysis (optional)… | Inquire |
| Methylation Analysis | 1. Basic bioinformatics analysis Sequencing Summary Alignment Summary List of peak positions identified by ChIP-seq tools Input data is transformed into applicable bam or wig format, as needed for visualization by commonly used genome browsers (e.g. IGV or UCSC Genome Browser) 2. Advanced bioinformatics analysis (optional) Medip Peak analyzer Customized Analysis(Cli… | Inquire |
| Whole Genome de novo Assembly | Sequencing Summary Pre-Assemble ( Error correction ) De novo Assembly ( contig, scaffold ) Consensus Polishing Gene prediction ( need RNA-seq data for Eukaryotes ) Genome plot 2. Advanced bioinformatics analysis (optional) De novo Assembly ( contig, scaffold ) Gene Annotation ( Gene Ontology ) Customized Analysis (Client Support) | Inquire |
genexa Ltd
Switzerlandgenexa is a genomic data analysis provider located in Switzerland. Our bioinformatics services are centered around de novo assembly of genomes and metagenomes. We focus on processing, analysis, and interpretation of your genomics data. For all our fields of expertise, we offer to perform the entire analysis workflow from raw data to documentation, but also consulting and troubleshooting if required. genexa also provides resources to run computationally demanding tasks for specific jobs if you have an existing analysis workflow, but lack the computational resources to run it on large amounts of data. For further information check: genexa.ch
Years in service: 9Other services offered by genexa Ltd:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Inquire | |
| Comparative Genome Analysis | Inquire | |
| Custom scripting and special projects | Inquire | |
| Other Services | We offer bioinformatics services using long-read sequencing (PacBio & Oxford Nanopore Technologies). We have several years of experience using third-gen. technologies, mainly applying these technologies for de novo assembly of individual genomes and metagenomes. We also offer transcriptomic analyses using long-read technologies. If you want to start using PacBio or Oxford Nanopore Technologies,… | Inquire |
| Read Filtering and Cleaning | Inquire | |
| Metagenomic Analysis | Inquire | |
| SNP / Indel Calling | Inquire | |
| Genome Annotation | Inquire | |
| Transcriptome Annotation | Inquire | |
| Variant Annotation | Inquire | |
| Whole Genome de novo Assembly | Inquire | |
| Base Calling | Inquire | |
| Microbiome Analysis | Inquire |
Cofactor Genomics
NGS provider United States of AmericaCofactor is focused on 3 main applications: RNA-sequencing, de novo assembly, and SNP/INDEL detection via resequencing. Over the last year, we have put significant R&D into our RNA-seq pipeline, and are now pleased to offer industry-leading protocols such as molecular spike-in controls, unprecedented QA/QC checks, ribosomal content screening, saturation analysis, and our ActiveSite Expression Viewer. These same protocols are also applied to our miRNA sequencing pipeline.
Other applications that fit well within our pipeline are: amplicon sequencing, custom capture and sequencing, 16S sequencing/microbiome sequencing, and highly custom projects.
Our scientists are happy to work with traditional model organisms, but we are experts in the more obscure. We've worked with nucleic acids from the complex field isolates, many plants including grapes, a variety of obscure animals including the Tardigrade (Water bear), and bacteria from multiple sources (micro biome, marine, biofuels, etc) to name a few.
While we are set-up to act as consultants, and support researchers throughout a full-service sequencing project, we are also happy to address the needs of more experienced researchers. Our expertise in library preparation or analysis may also be procured separate from the full-service offerings. And, those researchers who work with us in any capacity will have access to our team of scientists for support.
We have worked on small scale (1 sample) projects, all the way up through the larger, high throughput projects developed by big pharma. Every customer receives the same level of attentive, knowledgable customer service.
Years in service: 15Other services offered by Cofactor Genomics:
| Service | Description | Price |
|---|
Arizona Genomics Institute
NGS provider United States of AmericaThe Arizona Genomics Institute (AGI) offers DNA extraction, sequencing, and bioinformatic analyses. AGI has a two-decade long experience with isolation and purification of high-molecular weight DNA from plants and many other organisms. Since 2015, AGI is a PacBio Certified Service Provider, and currently operates the Sequel IIe instrument. Since the beginning of the genomics era, AGI has been a leader in genome analyses (BAC libraries, WGS sequencing, physical mapping) to the plant research realm, being the major lead in the rice and maize genome sequencing projects. So far, AGI's Service Center has developed more than 800 projects. Most of them are whole-genome shotgun sequencing projects, but a relevant part consists in Iso-Seq and amplicon sequencing projects. AGI has extensive experience in extracting high-molecular weight, highly-pure DNA for any sequencing application, from difficult plant, fungal, and metagenomic samples.
Years in service: 19Other services offered by Arizona Genomics Institute:
| Service | Description | Price |
|---|---|---|
| Genome Annotation | inquire for details | Inquire |
| Whole Genome de novo Assembly | inquire for details | Inquire |
Genome Explorations
NGS provider United States of AmericaGenome Explorations, Inc. is a premier research institution providing global genomic profiling and molecular diagnostics services to academic centers, pharmaceutical and biotech industry, oncologists, and pathologists with innovative diagnostic, prognostic, predictive, and personalized testing.
Our ‘Complete Solution’ requires you, our client, to only provide us with your biological samples (DNA, RNA, Cells, Tissue or Blood). Our highly trained staff subsequently process these samples to completion and analyze them using the latest advanced bioinformatics solutions. This model, combined with the one-on-one interactions we have with our investigators, allows us to generate the highest quality data sets in the industry.
We believe that the combination of unparalleled quality diagnostics, industry-leading innovation, and exceptional service enable us to help a range of clients develop and implement a personalized approach to healthcare and, ultimately, eradicate the most malicious disease states.
Years in service: 9Other services offered by Genome Explorations:
| Service | Description | Price |
|---|---|---|
| Differential Gene Expression Analysis | Inquire | |
| Whole Genome de novo Assembly | Inquire |