Metagenomic Analysis


Metagenomic analysis involves the application of bioinformatics tools to study the genetic material from environmental, uncultured microorganisms. Next generation sequencing of 16S rRNA allows the evaluation of bacterial diversity and detection of thousands of organisms. Analysis of metagenomic data involves three major steps: 1) assembly, 2) annotation, and 3) statistical analysis. If the goal is to analyze the genome of the microorganism rather than its community, short reads will have to be assembled into longer genomic contigs. Assembly approaches for metagenomic samples fall into two categories: reference based assembly and de novo assembly. Current metagenomic annotation relies on classifying sequences to known functions or taxonomic units based on homology searches against a database. Major annotation pipelines perform taxonomic assignments of reads.

Providers offering Metagenomic Analysis (found 17)

Wyzer Biosciences

NGS provider United States of America 16 years in service Metagenomic Analysis: $300.00 USD (per hour)
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Privately held, Wyzer Biosciences, Inc. was founded in 2011 and is located in dynamic Cambridge, MA, the home of Harvard, MIT and many other world-class educational and biotech institutions. Through our expertise in molecular biology we provide services to our partners and collaborators in industry and academia that will aid them in their ongoing research. Currently we are focusing on providing the Sanger, NGS (Illumina, Complete Genomics), Third-Generation (Nanopore) DNA sequencing and DNA prep services. Our company is ideally suited to solve your simple and complex sequencing needs. Over the years we have perfected all stages of Sanger sequencing workflow and are particularly well-equipped to deal with many types of difficult templates. Our strength is in fast and reliable double-strand sequence finishing, which includes primer design, contig assembly with editing and rudimentary data analysis. We provide inexpensive plasmid confirmation sequencing service that may be run on one or two platforms to get though difficult motifs and provide high quality data for the entire molecule. We provide various one-of-a-kind services along with the standard sequencing services. Our NGS and TGS services may include secondary bioinformatics analysis like data alignment to references and generation of consensus sequences. If you have some unique sequencing needs on small and medium scale, ask us. We will do our best to accommodate you. In the future we plan to expand our services and offer even wider choice of sequencing platforms and processes to better suit our customer’s needs.

Years in service: 16

Bioinformatics services offered by Wyzer Biosciences:

Service Description Price
Metagenomic Analysis Minimum Units: 1 Hour $300.00 USD (per hour)

CD Genomics

NGS provider United States of America 21 years in service Metagenomic Analysis: 120.00
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We specialize in the services of DNA sequencing, genotyping, DNA library construction and aptamer development. Shotgun Library Sequencing, cDNA Library Sequencing, SAGE Library Sequencing, Whole Genome Sequencing and Primer Walking Sequencing. we offer high quality Re-sequencing & SNP Discovery Services. Quite a few of our staff scientists once participated in the International HapMap Project too.

extensive experience in whole genome shotgun sequencing services. Beginning from bacterial cells or genomic DNA, we provide you with accurate genome consensus sequences. We are also experienced in genome annotation and comparative genomics research. Notably our staff scientists have finished a number of whole microbial genome sequencing projects, such as the genomes of Pseudomonas bathycetes, Bacillus thuringiensis, Thermoanaerobacter tengcongensis, Streptococcus suis, and quite a few virus genomes. In addition, our in-house Laboratory Information Management System (LIMS) as well as manual basecalling ensures the highest service quality.

CD Genomics has been offering professional DNA library construction services for over 5 years. Hundreds of various cDNA libraries (such as standard cDNA library, large insert cDNA library, normalized cDNA library and subtracted cDNA library) and genomic DNA libraries (including short-insert plasmid shotgun library, large-insert plasmid shotgun library, whole genome shotgun library, Fosmid library, Cosmid library, MiniBAC and BAC library) have been constructed in our lab

CD Genomics has been dedicated to provide a full range of services to develop high quality customized aptamers for research, diagnostic and therapeutic applications. Services offered by CD Genomics include aptamer synthesis, aptamer generation, cell aptamer selection, aptamer design and modification, negative selection and so on.

Years in service: 21

Bioinformatics services offered by CD Genomics:

Service Description Price
Metagenomic Analysis Key Features and Advantages Longest average read lengths, with~50% of reads longer than 50kb, which exceeds the size of repetitive elements in the average bacterial genome. No DNA amplification. Highest consensus accuracy, low sequencing-context bias Novel bioinformatics analysis programs and pipelines Well-experienced personnel Sample Requirements: gDNA≥5 ug Sequencing Strategy: PacBio Platfo… 120.00
Other Services We provide statistical and bioinformatic data analysis services that help explain the large amounts of data commonly generated by next generation sequencing and genotyping experiments. Our bioinformatic staff consists of all PhD-level scientists trained in bioinformatics, biology and statistics. The software infrastructure for analysis is a combination of custom-built and open-source software. O… Inquire
SNP / Indel Mapping CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost. Advantages of SNP Microarray Custom, flexible, and scalable; High call rates (> 99%) and high accuracy; Cost-… $80.00 USD (per sample)

Kovid BioAnalytics Pvt. Ltd.

India 13 years in service Metagenomic Analysis: $15.57 USD (per hour)
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Kovid BioAnalytics is an Informatics and Analytics company based in India. We specialize in building software, web-based or standalone applications for various bioinformatics projects, data curation and analysis services, etc. With a team of Bioinformatics experts and Software Developers we provide the following services: 1) Bioinformatics Software Development 2) Website Design and Maintenance for Bioinformatics Services 3) Curation of Genomics/Proteomics Data 4) Manual annotation of bioinformatics data and data mining 5) Technical writing services 6) Significance Analysis of micro-array data

Years in service: 13

Bioinformatics services offered by Kovid BioAnalytics Pvt. Ltd.:

Service Description Price
ChIP-Seq Analysis $20.00 USD (per hour)
Differential Gene Expression Analysis We have experience in performing Differential Gene Expression Analysis for various researchers from institutes like Washington University at St. Louis, West Mead Hospital (Australia), Spain Cancer Center and Bar Ilan University (Israel), etc. $16.57 USD (per hour)
Genome Annotation $15.00 USD (per hour)
Metagenomic Analysis We provide Metagenomic Analysis services including data curation as well as analysis. $15.57 USD (per hour)
Other Services We have a team of 5 experienced Bioinformatics Experts and 2 web developers, that can built custom pipelines for NGS data analysis, web applications, data mining tools, websites, etc. $16.57 USD (per hour)
Variant Annotation We provide variant annotation services that include manual annotation of variants using public databases as well as annotation through automated pipelines/tools like GEMINI. $16.57 USD (per hour)

Igenbio, Inc.

United States of America 13 years in service Metagenomic Analysis: 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

intelliseq

Poland Metagenomic Analysis: Inquire
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Bioinformatics services offered by intelliseq:

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

Genevia Technologies

Finland Metagenomic Analysis: 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

Computomics

Germany 14 years in service Metagenomic Analysis: Inquire
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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.

Years in service: 14

Bioinformatics services offered by Computomics:

Service Description Price
Comparative Genome Analysis We excel at managing complex crop genomic variance studies. Our analysis can help you obtain a set of genomic markers to enhance rational and controlled breeding procedures. Markers may include single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy number variations (CNVs) or structural variants (SVs). Taking into account the properties of your plant of interest and the … Inquire
Differential Gene Expression Analysis Gene expression studies, or RNAseq allow you to sequence the entire transcriptome of a plant, and provide valuable applications in crop improvement programs We and our collaborators have published peer reviewed methods for accurate gene expression analysis. Our RNAseq analyses can determine exact gene expression levels including splice variants. Using machine learning techniques, we identify dif… Inquire
Genome Annotation We perform de novo genome annotation using the latest in silico predictive approaches and RNAseq reads. We offer two machine learning-based gene prediction methods that can be trained to recognise biological features in your crop’s genome. The resources we use to build an annotation map include existing annotations for related organisms, RNAseq data, and PacBio complete isoforms. We use all avai… Inquire
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
Methylation Analysis Statistically Sound Epigenetics Non-genetic factors affect crops traits and phenotypes. Identifying epigenetic patterns allow breeders and plant scientists to uncover expression correlations and non-genetically inherited gene regulation patterns. We specialize in crop epigenetics. Methylation of cytosine residues is a known mechanism for gene silencing and gene expression regulation. We use bi… Inquire
Other Services Bioinformatics Consulting In addition to our next-generation sequencing (NGS) products and services, We also offer individual consulting services. With a team of scientists and partners who are thought leaders in crop genomics, we give impartial advice, independent of any sequencing platform, technology or tool suite. Each consultation is unique, please contact us to receive a quote for your sp… Inquire
Other Services Introgression and Insertion Delineation Next-generation sequencing is a great tool for molecular characterisation of seeds with genetic modifications or introgressions. We can provide answers to many regulatory and safety related questions, such as: At how many sites was the DNA integrated into the plant genome? What is the exact sequence of each insert? Is the sequence rearranged with respect t… Inquire
Other Services Genomic Selection with Continuous Model Improvement Genomic Selection with Continuous Model Improvement Genomic selection is a highly successful strategy to predict breeding values in plants. Advances in sequencing and high-throughput variant discovery enable the collection of tens of thousands of markers for hundreds of plants, providing exciting opportunities for unleashing the full power of g… Inquire
Read Filtering and Cleaning Inquire
Whole Genome de novo Assembly We have a deep understanding of both de novo and reference-based genome assembly of large crop genomes. It is crucial to first develop an effective strategy before selecting the appropriate sequencing technology and bioinformatics tools. A de novo genome assembly project must address sources of error up front, like sequence bias and read quality. A crucial point is quality control. We compare o… Inquire

Beckman Coulter Genomics

NGS provider United States of America 20 years in service Metagenomic Analysis: Inquire
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Beckman Coulter Genomics offers next generation sequencing services designed to meet the evolving sequencing needs of academic, biotechnology and pharmaceutical researchers worldwide. A comprehensive range of next generation sequencing services is available utilizing platforms from Illumina and Roche.

End to end solutions are offered allowing tailoring of projects to your specific needs. A wide variety of bioinformatics packages are available and results consultation is provided to ensure you understand the data returned to you. For the quickest service we accept pre-made libraries for sequencing only projects.

• Expert scientists consult on project design to ensure appropriate experimental approach • Beckman Coulter instrumentation utilized for fully automated library construction and target enrichment with enhanced reproducibility and reliability • Bioinformatics scientists oversee all data analysis to ensure quality
• Videoconference provided for report review and results discussion

Trusted Partner • Over 20 years sequencing experience • 1,500+ customer publications • 200+ successful audits • Experienced staff from well-known institutes of academic and commercial excellence • Contributed sequencing data to • >10 genome projects including mouse, cat, dog and salmon • >100 Microbial and Fungal genomes

Years in service: 20

Bioinformatics services offered by Beckman Coulter Genomics:

Service Description Price
Differential Gene Expression Analysis $150.00 USD (per sample)
Exome Analysis $250.00 USD (per sample)
Metagenomic Analysis Assembly including demultiplexing and standard run report Inquire
Read Filtering and Cleaning Inquire
Small RNA Annotation $150.00 USD (per sample)
SNP / Indel Calling $250.00 USD (per sample)
Targeted Capture Analysis $250.00 USD (per sample)
Variant Annotation $250.00 USD (per sample)

Omega Bioservices

NGS provider United States of America 14 years in service Metagenomic Analysis: $551.00 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 Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. $110.00 USD (per sample)
Differential Gene Expression Analysis Identify differentially expressed genes among samples using RNA-seq technique. Human, mouse, rat, fruit fly, cattle, pig, chicken, zebrafish, C. elegans, maize, thale cress, Japonica rice (Oryza sativa) and yeast, up to 7.5gb/sample. $56.00 USD (per sample)
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)

World Fusion US

United States of America 20 years in service Metagenomic Analysis: Inquire
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World Fusion is a well-established bioinformatics and cheminformatics software developer and services supplier with offices in Japan and the US. We have been at the forefront of developing genomic and drug discovery research tools since our early work on the Human Genome Project, and offer unparalleled reliability and expertise in our services.

Our customizable services include NGS data analysis, in-silico research services, and we are annotation specialists offering the most comprehensive correlations between genes, proteins, diseases, and chemicals.

The majority of the information is generated from our proprietary genomic and drug discovery research platform and knowledge base that we have been upgrading and building upon for over 10 years. It is comprised of original in-house data, curated information from over 60 top public data sets, and a chemical dictionary containing over 75 million non-redundant chemical compounds.

Our more recently added metagenomic and metaranscriptomic analysis services are carried out using state-of-the-art, original in-house software applications.

We offer MANY additional services, please contact us about your specific needs.

Years in service: 20

Bioinformatics services offered by World Fusion US:

Service Description Price
Genome Annotation Gene/Protein Annotation Services: • Identify relationships beween genes and proteins or diseases • Cite connections between genes or proteins and chemicals • Extract bind/inhibit chemicals from proteins or genes • Examine SNP information and association with disease • Find bind/inhibit compounds and therapeutic targets from associated disease • Gene expression prioritization from RNAseq dat… Inquire
Metagenomic Analysis 16S/28S/ITS rRNA metagenomic data analysis of the composition and diversity of microbial or fungal species from natural environments. Interactive HTML report with taxonomically classified charts & graphs, read counts, 2D, 3D, and interactive PCA plots, heat clustering maps, and self-organizing maps. •Metagenomic analysis of bacteria from species classification of taxonomic rank •Fungal metag… Inquire
Metagenomic Analysis Analysis of the transcripts present in the RNA-seq data through frequency analysis of functional categories from the selected protein DB (such as COG). Result files include annotations from ligand information with related chemical compounds, pathways, and iPath. •Biological function information •Metabolic compound info from proteins •Multiple sample analysis •Bar charts, pie charts, and fr… Inquire
Other Services Target Prioritization helps with the selection of gene/proteins for your research, from gene expression/SNV data - the analysis provides information about compounds and the activities, assays, SNPs, diseases, domains, pathways, and references. Inquire
Other Services In-silico target exploration from disease - therapeutic targets, related drugs, gene and protein targets, etc. Includes an extensive annotation table with information about the disease and related diseases, SNPs, compounds, drugs, genes, proteins, and tissues. Inquire
Other Services Target prediction from chemical structure - prediction of target proteins which is based on: 1.5M compounds, 5500 protein, and 5M interactions. Inquire
Transcriptome Annotation Expression data analysis includes over 20 kinds of annotation such as: genes (ontology, pathways), proteins, diseases, domains, ligands, and compounds. Prioritization of genes and proteins can be executed from a variety of directions. •Statistical processing from expression values •Conversion and active compound information from proteins •Inhibitor compounds and inhibitory active compounds … Inquire
Variant Annotation Analysis focuses on the SNP variant amino acid change and includes annotations of related diseases, genes, proteins, assays, ligands, SNPs, domains, and chemical compounds (active compound information, crystal structure, chemical formula, activities, etc.). •Non-synonomous SNPs and chemicals influenced by mutation location •Information about the compounds and proteins affected by the amino a… Inquire

CosmosID

United States of America 17 years in service Metagenomic Analysis: Inquire
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Shotgun Metagenomics Analysis: strain level resolution for bacteria, virus, fungi, protists Gene characterization: antibiotic resistance, virulence factors and function SNP analysis 16S / 18S / 23S / ITS amplicon analysis Whole Genome Sequencing Targeted Sequencing

Years in service: 17

Bioinformatics services offered by CosmosID:

Service Description Price
Metagenomic Analysis Metagenomic analysis of whole genome shotgun datasets using GENIUS® bioinformatics software and curated GenBook databases of bacteria, viruses, fungi, parasites and antibiotic resistance and virulence genes. Inquire
Microbiome Analysis CosmosID is a genomic big data company focused on rapid identification of microorganisms for infectious disease diagnostics, public health surveillance, food safety inspections, pharmaceutical discovery, and microbiome analysis for health and wellness. Prices decrease as sample volume increases. Inquire

Genotypic Technology

NGS provider India 28 years in service Metagenomic Analysis: $25.00 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 Metagenomic Analysis: $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 Metagenomic Analysis: 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

The Africa Genomics Centre and Consultancy (TAGCC) ltd

Kenya 12 years in service Metagenomic Analysis: Inquire
Contact Provider

TAGCC is an African company offering services in next generation sequence data analysis and consultancy in genomics. We have implemented a wide range of pipelines to analyse NGS data from various platforms including Illumina and 454. We support design and implementation of genomics and NGS based projects.

Years in service: 12

Bioinformatics services offered by The Africa Genomics Centre and Consultancy (TAGCC) ltd:

Service Description Price
Base Calling Demultiplex data and convert BCL or SFF files to FASTQ files. (Time is dependent on file size) $120.00 USD (per hour)
Differential Gene Expression Analysis We Identify differentially expressed and significant genes from RNA-seq data. Our workflow includes QC clean up, removal of ribosomal RNA contamination followed by denovo or reference based mapping. RPKM/FPKM-based quantitation. $80.00 USD (per sample)
Exome Analysis We analyse full exomes from raw sequence data through the process of cleaning, alignment, variant calling to analysis ready vcf file with variants effects summary. $125.00 USD (per sample)
Genome Mapping Alignment of NGS data to reference genome and generate mapping statistics $60.00 USD (per sample)
Metagenomic Analysis Generating publication ready Phylogenetic trees, Alpha and beta-diversity, rarefactions, rank abundance plots, relative abundance bar plots, with integration of meta-data, etc. Inquire
Other Services Admixture modelling and SNP phylogenetics. Use genetic data to infer the structure and evolutionary history of populations (Time is dependent on VCF/PED file size) $225.00 USD (per hour)
Read Filtering and Cleaning QC analysis, trimming and low quality reads removal. Both Raw and QC trimmed Fastq files will be made available. $24.00 USD (per sample)
SNP / Indel Calling Identify and qualify SNPs and Indels. $110.00 USD (per sample)
SNP / Indel Mapping Map SNPs and Indels. $110.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $110.00 USD (per sample)

genexa Ltd

Switzerland 11 years in service Metagenomic Analysis: Inquire
Contact Provider

genexa is a genomic data analysis provider located in Switzerland. Our bioinformatics services are centered around de novo assembly of genomes and metagenomes. We focus on processing, analysis, and interpretation of your genomics data. For all our fields of expertise, we offer to perform the entire analysis workflow from raw data to documentation, but also consulting and troubleshooting if required. genexa also provides resources to run computationally demanding tasks for specific jobs if you have an existing analysis workflow, but lack the computational resources to run it on large amounts of data. For further information check: genexa.ch

Years in service: 11

Bioinformatics services offered by genexa Ltd:

Service Description Price
Base Calling Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Differential Gene Expression Analysis Inquire
Genome Annotation Inquire
Metagenomic Analysis Inquire
Microbiome Analysis Inquire
Other Services We offer bioinformatics services using long-read sequencing (PacBio & Oxford Nanopore Technologies). We have several years of experience using third-gen. technologies, mainly applying these technologies for de novo assembly of individual genomes and metagenomes. We also offer transcriptomic analyses using long-read technologies. If you want to start using PacBio or Oxford Nanopore Technologies,… Inquire
Read Filtering and Cleaning Inquire
SNP / Indel Calling Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire

TAXON Bioinformatics Solutions S.A.

NGS provider 3 years in service Metagenomic Analysis: $280.00 USD (per sample)
Contact Provider

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 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 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 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)