Transcriptome de novo Assembly


Transcriptome de novo assembly is the process by which one uses RNA-Seq data to assemble a transcriptome without a reference genome. The lack of a reference genome is not an issue for RNA-Seq data sets as long as there are a sufficient number of paired end reads. First, reads from a next-generation sequencing dataset are combined and normalized to reduce read counts while maintaining read diversity and sample complexity. cDNA fragments are then assembled into transcripts using a short read assembler. Transcripts are assembled de novo by direct joining of overlapping reads into longer contigs. Protein coding regions can then be extracted from the assembly allowing for further characterization. The assembly can also be used to identify coding regions, or the measurement of abundance (expression). De novo transcriptome assembly is frequently the preferred method for examining non-model organisms as it is much cheaper than first building a reference genome.

Providers offering Transcriptome de novo Assembly (found 16)

Center for Bioinformatics and Functional Genomics (Miami University)

NGS provider United States of America 13 years in service Transcriptome de novo Assembly: $32.00 USD (per hour)
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We are a genomics and bioinformatics core facility located within Miami University in Oxford, Ohio, USA. We have an Illumina MiSeq Benchtop Sequencer; an ONT Nanopore minION, an epMotion 5073m NGS Liquid Handling Workstation; an ABI 3130xl Capillary Electrophoresis analyzer (Sanger), a Promega Maxwell16, Agilent Bioanalyzer2100, Sage BluePippin, Covaris M220 ultrasonicator, Qubit 4, Nanodrop (Fluorospectrometer) 3300, BioRad CFX Connect, QuantStudio7, RotorGeneQ (qPCR), several high capacity bioinformatics workstations equipped with both CLC Genomics Workbench and BioBam OmicsBox software, as well as many OS/FOSS software packages.

We are thus able to start from source material and isolate high quality nucleic acid, and construct libraries and perform appropriate QC at each step. We can perform NGS on either the Illumina MiSeq or the ONT minION, as well as comprehensive post-run bioinformatics analyses.

Years in service: 13

Bioinformatics services offered by Center for Bioinformatics and Functional Genomics (Miami University):

Service Description Price
Custom scripting and special projects Contact us about the possibility of a custom project/scripting for your problem. Inquire
Differential Gene Expression Analysis Project turnaround is number of samples dependent. Analysis of DGE using CLC Genomics Workbench GLM. Output is rich figures, graphs, heatmaps, tracks. Metadata is require prior to analyses. All data exported as CLC format and CSV (generic spreadsheet). Full report also included. $32.00 USD (per hour)
Microbiome Analysis 16S, 18S, ITS OTU analyses of amplicons - usually a 250 bp fragment size is used. SILVA, UNITE, MiDAS and Greengenes databases available. $32.00 USD (per hour)
Transcriptome Annotation Full transcriptome annotation via NCBI BlastX nr database, PFAM, and KEGG Pathways mapping. $300.00 USD (flat price)
Transcriptome de novo Assembly De novo transcription assembly; choose from an array of approaches/programmes - dependent on your needs and input data. $32.00 USD (per hour)

Igenbio, Inc.

United States of America 13 years in service Transcriptome de novo Assembly: Inquire
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Expertise:

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: 13

Bioinformatics services offered by Igenbio, Inc.:

Service Description Price
Base Calling Inquire
Comparative Genome Analysis Inquire
Differential Gene Expression Analysis 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
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
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
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Transcriptome Annotation Inquire
Transcriptome Annotation Inquire
Transcriptome de novo Assembly 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

Genevia Technologies

Finland Transcriptome de novo Assembly: Inquire
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Bioinformatics services offered by Genevia Technologies:

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

Bionivid Technology Private Limited

NGS provider India 15 years in service Transcriptome de novo Assembly: Inquire
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Whole Genome Sequencing, Transcriptome Sequencing (RNASEQ /miRNA), Metagenomics, Epigenomics, etc. to our credit; with 100+ co-authorship articles, highest in Indian industry. Recent past, we have also optimized multi-omics Single Cell Genomics solutions to cater to various research needs.

Years in service: 15

Bioinformatics services offered by Bionivid Technology Private Limited:

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

Biosof LLC

United States of America Transcriptome de novo Assembly: Inquire
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Bioinformatics services offered by Biosof LLC:

Service Description Price
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Differential Gene Expression Analysis Inquire
Genome Annotation Inquire
Genome Mapping Inquire
Read Filtering and Cleaning Inquire
SNP / Indel Calling Inquire
SNP / Indel Mapping Inquire
SNP/SV/CNV Discovery Inquire
Transcriptome Annotation Inquire
Transcriptome de novo Assembly Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire

Gringene Bioinformatics

New Zealand Transcriptome de novo Assembly: Inquire
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Bioinformatics services offered by Gringene Bioinformatics:

Service Description Price
Custom scripting and special projects Inquire
Differential Gene Expression Analysis Inquire
Genome Mapping Inquire
Other Services Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Mapping Inquire
Whole Genome de novo Assembly Inquire

Next Generation Intelligence

NGS provider Italy Transcriptome de novo Assembly: Inquire
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Bioinformatics services offered by Next Generation Intelligence:

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

Labindia-GPOD

India 16 years in service Transcriptome de novo Assembly: $500.00 USD (per sample)
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We 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: 16

Bioinformatics 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 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)
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)
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)

Omega Bioservices

NGS provider United States of America 14 years in service Transcriptome de novo Assembly: $553.00 USD (per sample)
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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: 14

Bioinformatics services offered by Omega Bioservices:

Service Description Price
Base Calling Demultiplex data and convert BCL files to FASTQ files $110.00 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)
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)
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)
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)
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)
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)
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)
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)
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)
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 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 / 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)
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)
Transcriptome Annotation Annotate or predict functions of transcribed genes using well know gene ontology tools. $332.00 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 Mapping Map mRNAs to either the reference or the assembled genome. $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)

Minnesota Informatics

United States of America 15 years in service Transcriptome de novo Assembly: Inquire
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Minnesota 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: 15

Bioinformatics services offered by Minnesota Informatics:

Service Description Price
ChIP-Seq Analysis Inquire
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
Read Filtering and Cleaning QC analysis, trimming and low quality masking/removal. 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 Annotation Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Mapping Inquire
Whole Genome de novo Assembly Bid will vary with type and size of genome. Inquire

Genotypic Technology

NGS provider India 28 years in service Transcriptome de novo Assembly: $600.00 USD (per sample)
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Genotypic 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: 28

Bioinformatics services offered by Genotypic Technology:

Service Description Price
Base Calling $20.00 USD (per hour)
ChIP-Seq Analysis $250.00 USD (per sample)
Custom scripting and special projects Bioinformatics support for 1 day - includes skype/webex consultation with detailed report. 120.00
Differential Gene Expression Analysis Differential Gene expressions, SNP variants and annotations with known reference, SSR discovery $69.00 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)
Metagenomic Analysis $25.00 USD (per sample)
Read Filtering and Cleaning $2.00 USD (per sample)
Transcriptome de novo Assembly Denovo transcriptome assembly with differential gene expression values. $600.00 USD (per sample)
Transcriptome Mapping $25.00 USD (per sample)
Whole Genome de novo Assembly $2900.00 USD (per sample)

TACGenomics

United States of America 11 years in service Transcriptome de novo Assembly: $100.00 USD (per sample)
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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: 11

Bioinformatics services offered by TACGenomics:

Service Description Price
ChIP-Seq Analysis $80.00 USD (per sample)
Custom scripting and special projects $50.00 USD (per hour)
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)
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)
Genome Mapping $50.00 USD (per sample)
Metagenomic Analysis $100.00 USD (per sample)
Methylation Analysis $100.00 USD (per sample)
Microbiome Analysis $50.00 USD (per sample)
Transcriptome de novo Assembly $100.00 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)
Whole Genome de novo Assembly $1000.00 USD (per sample)

ContigExpress, LLC

United States of America 16 years in service Transcriptome de novo Assembly: Inquire
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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: 16

Bioinformatics 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
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
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
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
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
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
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
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
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
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

ideas4biology Ltd.

Poland 13 years in service Transcriptome de novo Assembly: $250.00 USD (per sample)
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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: 13

Bioinformatics 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)
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)
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)
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 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)
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)
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)
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)
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 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)
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)

The Bioinformatics CRO

United States of America 8 years in service Transcriptome de novo Assembly: Inquire
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The Bioinformatics CRO is a scalable, globally distributed contract research organization and consultancy that provides high quality customized bioinformatics and genomics support to academics, biotechs, and pharmaceutical companies.

Years in service: 8

Bioinformatics services offered by The Bioinformatics CRO:

Service Description Price
ChIP-Seq Analysis Reveal the regulatory landscape of your genome. Our ChIP-seq experts identify binding sites, motifs, and epigenetic modifications with precision, linking protein-DNA interactions to transcriptional outcomes. We provide high-quality, publication-ready figures and data interpretation. Inquire
Comparative Genome Analysis See the bigger genomic picture. Our comparative genomics services uncover evolutionary relationships, genetic variation, and structural differences across species or strains. Clients trust us to translate raw sequence data into meaningful discoveries and competitive insights. Inquire
Custom scripting and special projects Your data, your vision, our expertise. Whether you need a bespoke analysis pipeline, multi-omics integration, or complete workflow automation, we design and implement solutions tailored to your research goals. Bring us your toughest challenge; we’ll turn it into results. Inquire
Differential Gene Expression Analysis Discover the genes that matter most. Our experts use industry-leading tools to pinpoint differential expression patterns and generate publication-ready insights. We go beyond basic outputs, delivering clear visualizations and biological interpretation that drive decision-making. Inquire
Other Services Find the genes that drive your system. We apply advanced co-expression network analysis (WGCNA and related methods) to identify hub genes, key modules, and regulatory networks. Perfect for biomarker discovery, drug target identification, and pathway prioritization. Inquire
Other Services Understand biology one cell at a time. From QC and clustering to cell-type annotation and trajectory inference, we deliver end-to-end single-cell RNA-seq and ATAC-seq analysis. Our team helps you uncover hidden cell populations and molecular programs that define disease or treatment response. Inquire
Transcriptome Annotation Bring biological meaning to your sequences. We integrate multiple databases and ortholog mapping strategies to deliver comprehensive, ready-to-publish transcriptome annotations. Our annotations enhance gene discovery, comparative analyses, and downstream functional studies. Inquire
Transcriptome de novo Assembly We reconstruct full transcriptomes from RNA-seq data to deliver high-confidence gene assemblies, even for non-model species. Expect accurate contigs, complete functional annotation, and differential expression analysis built on a solid foundation. Inquire
Transcriptome Mapping Turn your RNA-seq data into actionable results. We perform high-accuracy transcriptome mapping with optimized pipelines that maximize alignment efficiency and data quality. Reliable expression quantification and seamless integration with downstream analyses like DEG, splicing, and pathway enrichment. Inquire

TAXON Bioinformatics Solutions S.A.

NGS provider 3 years in service Transcriptome de novo Assembly: $250.00 USD (per sample)
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We are TAXON, a data-driven bioinformatics team, specializing in high-confidence downstream analysis and client-ready delivery (not just raw outputs). What makes us unique is that we package sequencing data into actionable, decision-oriented results using reproducible pipelines, ML-ready datasets, and regulatory-grade reporting when needed.

What we specialize

Plasmid-focused analysis: assembly/curation support (incl. circularization checks), plasmid typing/replicons, mobility elements, gene-level annotation, and optional AMR/virulence marker screening when needed.

Microbial genomics & taxonomy: strain identification, ANI/phylogenomics, contamination/QC, comparative genomics, and traceability/fingerprinting.

Metagenomics: end-to-end processing and interpretation for complex communities, including soil metagenomes and waste / residue-derived samples (taxonomic + functional profiling, group comparisons, biomarkers, ML-ready tables).

Yeast & fungal genomics: assembly/QC, annotation, comparative analyses, and applied interpretation for R&D.

Biosynthetic potential (BGC mining): detection, annotation, prioritization, novelty assessment, and clear "what to test next" guidance.

Scientific & regulatory-ready writing: structured, audit-friendly documentation and reports when clients operate in regulated markets.

Custom ML & data science (on request): we develop and productionize ML models for biological/biotech use cases (bioinformatics, AgTech), including feature engineering from omics data, biomarker discovery, predictive modeling, and deployment-ready datasets/pipelines.

Organisms & systems we've worked with

Bacteria and plasmids, including deep expertise in the Bacillus subtilis group and Bacillus cereus group, with published work on taxonomy across related species.

Yeasts and fungi, including Komagataella phaffii, Pichia pastoris and Trichoderma.

Mixed microbial communities (microbiomes), especially from soil and natural environments.

Years in service: 3

Bioinformatics services offered by TAXON Bioinformatics Solutions S.A.:

Service Description Price
Base Calling Conversion of raw sequencing signal data into FASTQ files. Includes base calling, basic read quality assessment, and organized FASTQ delivery. Demultiplexing or additional QC can be included if specified in the project scope. 170.00
Comparative Genome Analysis Comprehensive comparative genome analysis across strains, species, or reference datasets. This service may include comparative gene content analysis, functional clustering, broader gene presence/absence screening, antiSMASH/BGC comparison, selected phylogenomic analyses, figures, summary tables, and a detailed technical report. Recommended for projects requiring biological interpretation beyond a… $665.00 USD (per sample)
Comparative Genome Analysis Comparative analysis of genomes or selected genomic features across strains, species, or reference datasets. This service may include ANI analysis, selected BLAST comparisons, gene presence/absence screening, basic phylogenetic placement, and summary tables. It is intended for focused comparisons with a limited number of genomes or predefined targets. Price per comparison 450.00
Custom scripting and special projects Custom bioinformatic scripting, workflow development, data parsing, figure generation, file conversion, automation, or ad hoc analysis not covered by standard services. Turnaround depends on scope and data complexity. $110.00 USD (per hour)
Differential Gene Expression Analysis Differential expression analysis between experimental conditions from a count matrix or normalized expression table. Includes statistical analysis, fold-change and significance tables, volcano/MA plots, PCA or clustering plots when appropriate, and a concise report. FASTQ processing and transcriptome mapping are quoted separately. Price per comparison 335.00
Genome Annotation Structural and functional annotation of prokaryotic genomes. Includes gene prediction, CDS annotation, rRNA/tRNA detection, functional assignment, GFF/GenBank/FASTA output files, annotation tables, and a concise technical report. $199.00 USD (per sample)
Genome Annotation Basic structural and functional annotation of simple eukaryotic genomes, such as yeasts or small fungal genomes. Includes gene prediction/annotation when suitable input data are available, functional assignment, GFF/GenBank/FASTA output files, annotation tables, and a concise technical report. Complex eukaryotic genomes, large genomes, or projects requiring transcriptome-guided/manual annotation … $399.00 USD (per sample)
Genome Mapping Alignment of genomic sequencing reads to a reference genome. Includes read mapping, alignment quality metrics, coverage summary, sorted/indexed alignment files, and a brief report. Variant calling or biological interpretation is not included unless requested separately. $220.00 USD (per sample)
Metagenomic Analysis Bioinformatic analysis of previously generated metagenomic sequencing data. Includes read quality control, filtering, taxonomic profiling, abundance tables, diversity summaries when applicable, and a concise report. Functional profiling may be included depending on data type and sequencing depth. $280.00 USD (per sample)
Microbiome Analysis Bioinformatic analysis of amplicon-based microbiome data, such as 16S, ITS, or similar marker-gene sequencing. Includes quality filtering, denoising/ASV or OTU inference, taxonomic assignment, abundance tables, alpha/beta diversity summaries, plots, and a brief report. $280.00 USD (per sample)
Other Services Bioinformatic consulting or custom analysis outside the listed service categories. Scope, deliverables, and turnaround are defined before project start. $110.00 USD (per hour)
Read Filtering and Cleaning Quality control and preprocessing of sequencing reads. Includes adapter trimming, low-quality read filtering, quality reports, cleaned FASTQ files, and a brief QC summary. Host/contaminant removal can be included if reference files are provided or specified. $110.00 USD (per sample)
SNP / Indel Calling Detection of SNPs and small insertions/deletions relative to a reference genome. Includes mapping review, variant calling, basic filtering, VCF file generation, variant summary tables, and a short technical report. $335.00 USD (per sample)
SNP / Indel Mapping Mapping of sequencing reads against a reference genome for downstream SNP and small indel analysis. Includes read alignment, sorting/indexing, basic alignment quality control, and delivery of BAM/CRAM files plus a short QC summary. $220.00 USD (per sample)
SNP/SV/CNV Discovery Discovery of SNPs, indels, structural variants, and/or copy number variation depending on the available sequencing data and reference genome quality. Includes variant tables, filtered output files, summary statistics, and a technical report. $450.00 USD (per sample)
Transcriptome Annotation Functional annotation of assembled eukaryotic transcripts or transcript sequences. Includes ORF prediction when applicable, similarity searches, domain/function assignment, annotation tables, and a concise technical report. Complex transcriptomes, non-model organisms, or large datasets may require custom pricing. $399.00 USD (per sample)
Transcriptome Annotation Functional annotation of assembled prokaryotic transcripts or transcript sequences. Includes ORF prediction when applicable, similarity searches, domain/function assignment, annotation tables, and a concise technical report. $199.00 USD (per sample)
Transcriptome de novo Assembly De novo assembly of transcriptomic reads without a reference genome. Includes read QC, transcript assembly, assembly quality statistics, transcript FASTA files, and a technical summary. Annotation is not included unless requested separately. $250.00 USD (per sample)
Transcriptome Mapping Mapping of RNA-seq reads to a reference genome or transcriptome. Includes read alignment, alignment QC, gene/transcript quantification when annotation is available, count/TPM tables, BAM files, and a short technical summary. $225.00 USD (per sample)
Whole Genome de novo Assembly De novo genome assembly from sequencing reads. Includes read QC, assembly generation, assembly quality statistics, contamination/quality checks when applicable, FASTA output, and a brief technical report. Complex eukaryotic genomes or hybrid assemblies may require custom pricing. $199.00 USD (per sample)