Methylation Analysis


Methylation of cytosine bases are common epigenetic marks that have important implications for normal biological processes and disease. Computational tools for analyzing and interpreting DNA methylation data can be broken down into three broad steps:

  1. Data processing and quality control
  2. Transformation of raw data into methylation maps
  3. Visualization of DNA methylation data and statistics to identify sample specific differences
  4. Computational methods to assist in validating differences in methylation and their interpretation

The processing of bisulfite sequencing data includes sequence alignment and the quantification of absolute DNA methylation at base resolution. Visualization of selected regions can be done on a genome browser. This aids in examining global distribution of DNA methylation. Clustering analysis and differences in sets of samples can also be performed. The validation of differentially methylated regions (DMRs) can be performed manually or using a number of different automated computational rankings.

Providers offering Methylation Analysis (found 18)


Omega Bioservices

NGS provider United States of America

Our 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: 7

Other services offered by Omega Bioservices:

Service Description Price
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)
Differential Gene Expression Analysis Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. $110.00 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 are open to your custom analysis projects. Set up a call with our Project Scientist team today to discuss your needs and obtain a quote. $500.00 USD (per sample)
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)

TACGenomics

United States of America

TACGenomics 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: 5

Other 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)

ideas4biology Ltd.

Poland

DATA ANALYSIS Routine NGS data analysis in the area of genomics and transcriptomics, such as: - Gene expression and differential expression analysis - De novo and ab initio transcriptome assembly - Small RNA analysis - Genome variant calling and annotation

Customized tasks, including: - Identification of long noncoding RNAs - Identification of ta-siRNAs - Isomir and miRNA editing analysis - Annotation of non-model organisms - Building transcriptome-wide maps of RNA-RNA interactions

WORKSHOPS We offer workshops in a broad spectrum of bioinformatics applications, including: - RNA-Seq data analysis (4 days) - NGS in medical research (4 days)

EXPERIENCE We’ve been in the market since 2013 and came into collaboration with hundreds of customers. We’ve been working on model and non-model organisms, including viruses, bacteria, fungi, plants, animals, and human. We are part of research consortium aiming at development of personalized medicine services for diagnosis and treatment of lung cancers. We are also actively conducting research projects in different areas of genomics and transcriptomics, which gives us expertise in standard and up-to-date bioinformatics solutions.

INFRASTRUCTURE We have access to dedicated file storage and computational servers, with virtually unlimited (on demand) capacity.

Years in service: 6

Other services offered by ideas4biology Ltd.:

Service Description Price
Differential Gene Expression Analysis This includes: - quality filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping - expression estimation - differential expression analysis - a report, result data files and diagnostic plots Differential expression analysis itself, with expression estimations from customer: $30. $185.00 USD (per sample)
Transcriptome Mapping This includes: - quality check and filtering - adapter trimming - optional: discarding rRNA-mapping reads and other contaminants - read mapping (default or customized settings) - read mapping report and result files $100.00 USD (per sample)
Other Services Identification of long noncoding RNAs in animals and plants. This includes: - assessment of protein-coding potential with at least two independent methods - sequence length filtering - discarding of known, coding transcripts - discarding known noncoding RNAs other than lncRNAs - optionally: genomic context-driven filters - other filtering steps, depending on data availability, such as tran… $50.00 USD (per hour)
Read Filtering and Cleaning This includes: - Quality report - Quality filtering - Adapter trimming - Optionally: discarding rRNA-mapping reads or other contaminants $46.00 USD (per sample)
Small RNA Mapping This includes: - quality check and filtering - adapter trimming - read mapping to custom sequences (genome, transcriptome) - read mapping quality assessment - read mapping report This may be followed by miRNA identification or similar tasks, priced separately. $130.00 USD (per sample)
Genome Mapping This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping with varied tools and settings - accomodated to customer's needs - quality report $85.00 USD (per sample)
SNP / Indel Calling This includes: - quality check and filtering - adapter trimming - read mapping and further processing of mapping results - SNP / Indel calling Both somatic and germline variants may be called. There is possibility to call structural variants as well, priced separately. $165.00 USD (per sample)
Small RNA Annotation This includes: - quality check and filtering - adapter trimming - read mapping to databases of noncoding RNAs, such as miRBase, DASHR or RFAM - annotation report $150.00 USD (per sample)
Methylation Analysis This includes: - quality check and filtering - adapter trimming - read mapping - calling methylated and unmethylated cytosines - differential methylation analysis: finding differentially methylated bases and regions $250.00 USD (per sample)
Transcriptome de novo Assembly This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - transcriptome de novo assembly - a quality report and a transcriptome in FASTA format For further annotation of the transcriptome, please see our offer for "Transcriptome annotation". $250.00 USD (per sample)
Transcriptome Annotation This includes: - BLAST searches against databases of proteins and noncoding RNAs, including miRBase, RFAM, UniProt (Swiss-Prot) - hmmscan search against PFAM protein domains - assignment of GO terms to genes - assignment of KEGG pathways to genes - a report and annotation files with per gene details $125.00 USD (per sample)
Variant Annotation This includes: - prediction of possible consequences associated with predicted variants, such as affecting splicing of protein coding capacity - comparison with known variants from public databases - a report and result files $150.00 USD (per sample)

Parseq Lab

Czechia

Parseq 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: 8

Other services offered by Parseq Lab:

Service Description Price

Zymo Research

NGS provider United States of America

Zymo Research makes genome-wide epigenetic analyses available to every researcher with its comprehensive repertoire of services. All Next-Gen epigenetic sequencing services feature state-of-the-art sample prep technologies and workflows, cutting-edge bioinformatics, and are offered at competitive pricing. With our services, you don't have to be a bioinformatics guru; instead, our bioinformatics specialists will send you the data as a comprehensive report that is publication-ready and can be customized to fit your needs. Since we develop most of the technologies used for our services, our scientists and bioinformatics specialists are always available to answer your questions and assist you every step of the way.

Our Methyl-MiniSeq™ platform is based on an expanded reduced representation bisulfite sequencing (RRBS) protocol that allows genome-wide profiling of 5-methylcytosine (5-mC). Additionally, we can also work on a wide range of sample types including any species with a reference genome, low-input (>10 ng), and FFPE samples.

Our Reduced Representation Hydroxymethylation Profiling (RRHP) service is for genome-wide profiling of 5-hydroxymethylcytosine (5-hmC) in DNA at single-nucleotide resolution, and is the only such service available. RRHP also allows strand-specific determination of the location of the 5-hmC modification, as well as quantification of 5-hmC levels. Data from RRHP is easily integrated with DNA methylation data from Methyl-MiniSeq™, allowing for direct comparison of DNA methylation and hydroxymethylation in the same sample.

Years in service: 8

Other services offered by Zymo Research:

Service Description Price
SNP / Indel Calling Inquire
Genome Annotation Inquire
Methylation Analysis Basic bioinformatic analysis is provided and includes raw data alignment, variant calling (differential methylation and/or hydroxymethylation and SNP detection), and gene/locus annotation. Additional, complete, and customizable bioinformatic analysis is also available. Inquire

Next Generation Intelligence

NGS provider Italy

NGI is a platform for Next Generation Sequencing data analysis. We offer a wide range of bioinformatics tools and an experienced and professional collaboration service for any type of biological data analysis. We provide both standard and customized analysis, custom softwares and pipelines development and post-sequencing support. We'll enhance and make easier your discovery process.

Expertise:

Our expertise is in the epigenetics field in mouse and human organisms.

Infrastructure:

we will provide FTP access to our storage server to upload raw data and download analyzed data.

Other services offered by Next Generation Intelligence:

Service Description Price
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
Base Calling Inquire
Targeted Capture Analysis Inquire
Differential Gene Expression Analysis Inquire
Genome Mapping Inquire
Small RNA Mapping Inquire
Exome Analysis Inquire
Transcriptome Mapping Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Custom scripting and special projects Inquire
Transcriptome de novo Assembly Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Small RNA Annotation Inquire
SNP/SV/CNV Discovery Inquire
Methylation Analysis Inquire
ChIP-Seq Analysis Inquire
Variant Annotation Inquire

Computomics

Germany

Bioinformatics 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.

Our vast crop and plant experience encompasses Maize, wheat, barley, rice, soybean, canola, sorghum, triticale, potato, cotton, switchgrass, watermelon, lettuce, spinach, melon, banana, cocoa, coffee, sugar cane, cucumber, alliums, brassica, chickpea, pepper, papaya, medicago, lotus, hops, sugar beet, tomato, poplar, pine, as well as plant viruses, algae, fungi, soil and leaf metagenomics.

Years in service: 7

Other services offered by Computomics:

Service Description Price
Read Filtering and Cleaning Inquire
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 Computomics 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 i… 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. Computomics specializes in crop epigenetics. Methylation of cytosine residues is a known mechanism for gene silencing and gene expression regulat… Inquire
Genome Annotation Computomics performs 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 u… Inquire
Whole Genome de novo Assembly Computomics has 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. W… 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… Inquire
Other Services Bioinformatics Consulting In addition to our next-generation sequencing (NGS) products and services, Computomics also offers 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 quo… 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
Comparative Genome Analysis Computomics excels 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 intere… Inquire
Other Services Introgression and Insertion Delineation Next-generation sequencing is a great tool for molecular characterisation of seeds with genetic modifications or introgressions. Computomics 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 wit… Inquire

ecSeq Bioinformatics

Germany

Bioinformatics solutions

ecSeq provides a variety of bioinformatics service packages suited for most everyday high-throughput sequencing experiments. We are particularly engaged in RNA-seq projects (trancriptomics, differential expression), ncRNA analysis (small RNA-seq, ncRNA annotation) and epigenome sequencing (bilsufilte and methylation analyses). Further bioinformatics solutions include SNP calling, variant annotation & prioritisation as well as development of customized algorithms.

Public workshops and eTrainings

We develop eTrainings and provide workshops for employee training in bioinformatics. Several times a year, we organize well-attended workshops on selected topics in next-generation sequencing data analysis. Test datasets are used for getting started in applying and developing bioinformatic tools.

Topics covered by our workshops include:

  • RNA-seq bioinformatics
  • Sequencing technolgies
  • Small RNA-seq data analysis
  • Genomic data visualization
  • Perl for bioinformatics
  • Programming in R

Expertise:

We have long experience in the development and application of bioinformatics methods to high-throughput sequencing experiments. These methods have been successfully applied in various experimental designs ranging from ncRNA and mRNA sequencing to genome/epigeome analyses. We have worked with sequencing data from humans, lifestock species (chicken, cow, turkey), plants and bacteria. Our employees are continuously involved in projects from national and international consortia, like the International Cancer Genome Consortium (ICGC) or the Leipzig Research Centre for Civilization Diseases (LIFE).

Infrastructure:

We have access to moderate computation resources allowing us to process ~120GB sequence data per week.

Other services offered by ecSeq Bioinformatics:

Service Description Price
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
ChIP-Seq Analysis Inquire
Genome Mapping Inquire
Variant Annotation Inquire
Small RNA Mapping Inquire
Transcriptome Mapping Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Custom scripting and special projects Inquire
SNP / Indel Mapping Inquire
Transcriptome Annotation Inquire
Differential Gene Expression Analysis Inquire
Exome Analysis Inquire
SNP/SV/CNV Discovery Inquire

ContigExpress, LLC

United States of America

ContigExpress 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: 10

Other services offered by ContigExpress, LLC:

Service Description Price
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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

NXT-Dx

NGS provider Belgium

At NXT-Dx we can offer SE50, PE50 and PE100 sequencing on the Illumina HiSeq. On top of this we can also offer different sequencing settings on the Illumina MiSeq and shortly we will also be able to offer sequencing on the Illumina NextSeq.

We can offer sequencing of already prepared libraries but we can also offer full-scope projects whereby we receive cells, tissue, gDNA or RNA and take care of the sample preparation, library prep, sequencing and bio-informatics analysis.

We have worked with samples from all kind of species (mammalian, plant, bacterial) and all kind of cell types.

We pride ourselves in having close contact with our customers and only one single contact point. Also after the delivery of the data, we remain available to answer any questions customers might have on their data, their analysis, etc.

Years in service: 8

Other services offered by NXT-Dx:

Service Description Price
Differential Gene Expression Analysis $170.00 USD (per hour)
Transcriptome Mapping $170.00 USD (per hour)
Comparative Genome Analysis $170.00 USD (per hour)
Custom scripting and special projects $170.00 USD (per hour)
Read Filtering and Cleaning $170.00 USD (per hour)
Exome Analysis $170.00 USD (per hour)
ChIP-Seq Analysis $170.00 USD (per hour)
Small RNA Mapping $170.00 USD (per hour)
Genome Mapping $170.00 USD (per hour)
Targeted Capture Analysis $170.00 USD (per hour)
Genome Annotation $170.00 USD (per hour)
Small RNA Annotation $170.00 USD (per hour)
Methylation Analysis $170.00 USD (per hour)
Transcriptome Annotation $170.00 USD (per hour)
Variant Annotation $170.00 USD (per hour)
Base Calling $170.00 USD (per hour)

SciBerg

Germany

We offer computational analyses of Next-Generation Sequencing data (Illumina and Ion Torrent platforms), including RNA-seq, small RNA-seq, DNA-seq, Bisulfite-seq and ChIP-seq. Our bioinformatics support can be fully customized for your research needs, the scope and objectives of the study. We apply only up-to-data well-proven software and pipelines working under Unix/Linux environment. Optionally, our experts can help to interpret the obtained results from the scientific point of view, provided some of them are working in a close research field.

Other services offered by SciBerg:

Service Description Price
Differential Gene Expression Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Exome Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
ChIP-Seq Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Methylation Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire

DREAMgenics

NGS provider Spain

We offer bioinformatics analysis services for human and other organisms genomic and transcriptomic NGS data.

  • Our team of experts offers a completely personalized consulting service, including scientific and technical solutions to your needs. We help you to obtain the best results from your analysis.

  • Our collaboration with the most reliable sequencing providers allow us to select the most suitable platform for your project. We also can assist you in all steps prior to sequencing, such us sample and library preparation and quality controls.

  • DREAMgenics bioinformatics framework has been designed to readily adapt to your needs. Capable of integrating your own algorithms, pipelines and databases to complement the data analysis and interpretation.

  • Our analyses identify high quality genomic variants through excellent sensitivity and specificity standards, extracting meaningful biological information and reducing validation process costs. The results will be delivered through a detailed report.

  • We offer the possibility of advanced visualization and interactive review of results through our exclusive DG Reports web application. (Filtering and priorization of variants, Pre-classification of variants, Graphic interface (genomic browser), Statistics and quality controls, Exportable information, Automated generation of reports).

All our procedures meet with the requirements set by the new General Data Protection Regulation.

Years in service: 8

Other services offered by DREAMgenics:

Service Description Price
ChIP-Seq Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Exome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Base Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Comparative Genome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Custom scripting and special projects https://www.dreamgenics.com/en/bioinformatics-services/ https://www.dreamgenics.com/en/research-projects/ Inquire
Other Services - Research projects https://www.dreamgenics.com/en/research-projects/ - Bioinformatics software design and developments https://www.dreamgenics.com/en/hd-genome-one-en/ - Gene and/or regions of interest panels, ATAC Seq, Family studies, trio analysis.. https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Differential Gene Expression Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Metagenomic Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Methylation Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Microbiome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Read Filtering and Cleaning https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP/SV/CNV Discovery https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Targeted Capture Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Variant Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Whole Genome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire

Igenbio.Inc

United States of America

Expertise:

  • Genome ORF calling: Eukaryotes and Prokaryote Genomes
  • Annotations
  • Pathway Analysis
  • Metabolic Reconstruction
  • SNP Analysis
  • Comparative Genomics
  • Integration of GWAS expression data onto genomes and pathways

Infrastructure:

Data is stored in house with a dedicated server room with 24/7 security. We compute using our proprietary algorithms internally and curate the genomes with comparative analysis platform. We have over 2,600 genomes in the data base which are manually curated. Access is provided via web or server access.

Years in service: 6

Other services offered by Igenbio.Inc:

Service Description Price
SNP / Indel Mapping Inquire
Transcriptome Annotation Inquire
SNP / Indel Calling Inquire
Genome Mapping Inquire
Variant Annotation Inquire
Comparative Genome Analysis Inquire
Metagenomic Analysis Inquire
Genome Annotation Inquire
Methylation Analysis Inquire
Custom scripting and special projects Inquire
Whole Genome de novo Assembly Inquire

HybridStat Predictive Analytics

Greece

HybridStat 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: 5

Other 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 $20.00 USD (per sample)
Read Filtering and Cleaning $25.00 USD (per sample)
Read Filtering and Cleaning $30.00 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)
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)
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. $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. $100.00 USD (per sample)
SNP / Indel Mapping $40.00 USD (per sample)
SNP / Indel Mapping $25.00 USD (per sample)
SNP / Indel Mapping $30.00 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 $50.00 USD (per sample)
SNP / Indel Calling $45.00 USD (per sample)
SNP / Indel Calling $40.00 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)
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. $40.00 USD (per sample)
Whole Genome de novo Assembly $1000.00 USD (flat price)

Strand Life Sciences

India

Strand Life Sciences is a technology innovation company that has pioneered the practice of scientific intelligence in health sciences. Strand was established in 2000, with a founding theme “Algorithms for Life”. The company is an academic-spin of in India, founded by four Computer Scientists - Dr. Vijay Chandru, Dr. Ramesh Hariharan, Dr.V. Vinay, and Dr. Swamy Manohar. Since then, we have established a strong portfolio of products for biological systems research and for diagnosis and treatment of diseases. Over 2000 scientific laboratories and 100 hospitals across the world are our clients. Now, we have entered a new era guiding medical decisions using molecular insights with a new theme ‘New Generation Healthcare’.

Strand NGS-Formerly Avadis® NGS is Strand’s flagship product for analysis, management and visualization of next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, ChIP-Seq, MeDIP-Seq and Methyl-Seq experiments. We provide bioinformatics services using Strand NGS and price is dependent on man hours, number of samples and other factors. Please consult us for more details sales@strandngs.com

Years in service: 9

Other services offered by Strand Life Sciences:

Service Description Price
ChIP-Seq Analysis Inquire $500.00 USD (per sample)
Differential Gene Expression Analysis $500.00 USD (per sample)
Exome Analysis $500.00 USD (per sample)
Methylation Analysis $500.00 USD (per sample)
SNP/SV/CNV Discovery $500.00 USD (per sample)
SNP / Indel Calling $500.00 USD (per sample)
SNP / Indel Mapping $500.00 USD (per sample)

intelliseq

Poland

I approach analytic challenges creatively with the result being novel, statistically significant and reproducible. I have high expertise on differential expression using RNA-seq.

Expertise:

I've been working with whole genome experiments for the last 10 years. I analysed more than 1000 gene expression microarrays (Illumina and Affymetrix, Human, Mouse, Rat and Pig). I analysed RNA-seq samples (total RNA and polyA RNA) from SOLiD 5500xl and Ion Proton, ChIP-seq samples from Illumina HiSEQ and DNA-seq (Exome) samples from Illumina HiSEQ. I developed several tools for functional analysis (see cremag.org) of gene lists.

Infrastructure:

I have almost unlimited access to Amazon EC2 and large server on site (two 8x core Xeon with 216 GB RAM 64GB of SAS disks)

Other services offered by intelliseq:

Service Description Price
Transcriptome Annotation Inquire
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
ChIP-Seq Analysis Inquire
Differential Gene Expression Analysis Inquire
Variant Annotation Inquire
Transcriptome Mapping Inquire
Metagenomic Analysis Inquire
Methylation Analysis Inquire
Custom scripting and special projects Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Small RNA Mapping Inquire
Genome Annotation Inquire

Epigentek

NGS provider United States of America

We specialize in end-to-end epigenetic-related NGS services, primarily Methyl-Seq (RRBS and WGBS) and ChIP-Seq as well bioinformatics analysis. Our competitive pricing, paired with our extensive epigenetic product expertise since 2005, allows us to build optimized libraries to deliver accurate data and results.

Years in service: 5

Other services offered by Epigentek:

Service Description Price
ChIP-Seq Analysis 1) Raw data: Illumina FASTQ file(s) 2) Analysis workflow a. Data quality control b. Read mapping c. Peak calling $828.75 USD (per sample)
Methylation Analysis 1) Raw data: Illumina FASTQ file(s) 2) Analysis workflow a. Data quality control b. Read mapping c. Methylation calling d. Sample correlation and clustering $552.50 USD (per sample)

Genevia Technologies

Finland

Genevia Technologies provides a wide range of microarray and next generation sequencing data analyses, and bioinformatics services to life science companies and academia. In addition, we offer bioinformatics consulting projects at a fixed price, and genome-wide experiments done in collaboration with the top service providers.

Expertise:

Our expertise is in handling multiple microarray (expression, copy number, ChIP, methylation, etc) and next-gen sequencing (DNA-seq, RNA-seq, MeDIP-seq, ChIP-seq, GRO-seq, etc) data simultaneously and effectively, and combining them with other data such as clinical variables or pathway information. We have experience in most common mammalian systems, but especially in multiple human cancers. We have also worked on data from multiple species of lower eucaryotes and bacteria.

Infrastructure:

We have access to dedicated file storage servers, a computing cluster, a computing grid (of over 1000 CPUs), and cloud computing capabilities.

Visit our homepage to read more about us and our bioinformatics as a service: www.genevia.fi

Other services offered by Genevia Technologies:

Service Description Price
Methylation Analysis Inquire
SNP / Indel Calling Inquire
Base Calling Inquire
ChIP-Seq Analysis Inquire
Targeted Capture Analysis Inquire
Variant Annotation Inquire
Small RNA Mapping Inquire
Comparative Genome Analysis Inquire
Small RNA Annotation Inquire
Transcriptome Annotation Inquire
Custom scripting and special projects Inquire
SNP/SV/CNV Discovery Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Read Filtering and Cleaning Inquire
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Metagenomic Analysis Inquire
Transcriptome de novo Assembly Inquire