Microbiome Analysis


Involves the analysis of microbial communities using bioinformatics tools. These include analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences.

Providers offering Microbiome Analysis (found 11)


Applied Biological Materials Inc.

NGS provider Canada

Committed to making newer technologies attainable to modern researchers, abm offers a wide range of sequencing services on the advanced Illumina® sequencing platforms at accessible prices and rapid turnaround times. abm's premium NGS services will not only save valuable time and money, but also provide the most reliable and comprehensive solution for the project's needs.

Advantages of using our NGS services: -dedicated NGS specialists to help with experimental design and data analysis -customizable bioinformatics analysis to suit your project needs -strict quality control at multiple steps in library preparation and sequencing -RNA-seq, miRNA-seq, WGS, metagenomics, epigenetics, Amplicon-Seq and more!

What types of bioinformatics analysis will be done? If the reference genome is available (i.e. human or mouse), read mapping and alignment to the reference genome is included in the service. -Data is available in industry standard formats: FASTQ (default), SFF or BAM. Other formats available upon request (additional fees may apply). -RNA-seq includes: Read mapping and gene expression level estimation

Our data report files are provided in formats that can be viewed with any standard text viewers.

Years in service: 6

Other services offered by Applied Biological Materials Inc.:

Service Description Price
Differential Gene Expression Analysis Service includes: 1) Principal component analysis; 2) Differential gene expression analysis; 3) Gene expression clustering; 4) Full analysis report $222.00 USD (per sample)
Exome Analysis Service includes: 1) Read mapping; 2) deduplication, local realignment and base recalibration; 3) Variation calling; 4) Variation annotation (dbSNP, COSMIC, ClinVar, 1000 Genome); 5) Full analysis report $95.00 USD (per sample)
Metagenomic Analysis Service includes: 1) Contig assembly; 2) OTU clustering and classification; 3) Alpha/beta diversity analysis; 4) Full analysis report; $35.00 USD (per sample)
SNP / Indel Calling Service available for WGS and WES to include: 1) Read mapping; 2) De-duplication, base quality recalibration, and local realignment; 3) SNP and Indel calling $225.00 USD (per sample)
Genome Annotation Service includes: 1) Gene prediction; 2) Functional annotation from KEGG, GO, NCBI $333.00 USD (per sample)
Whole Genome de novo Assembly Service for De novo assembly of genome size < 10Mb. $350.00 USD (per sample)
Microbiome Analysis Service includes: 1) Contig assembly; 2) OTU clustering and classification; 3) Alpha/beta diversity analysis; 4) Full analysis report; $35.00 USD (per sample)

Parseq Lab

Czechia

Parseq Lab is experienced in: - massively parallel sequencing data analysis - client-tailored algorithms and software development - analysis pipelines deployment

We offer: - whole genome/exome and targeted sequencing data analysis - de novo assembly - SGV detection and annotation - expression analyses - metagenomics analysis - transcriptomics analysis - proteomics research - genuine task-specific workflows design - custom bioinformatics applications development - statistical data analysis

Collaborations: genomic research labs, sequencing facilities, academic and research institutions.

Years in service: 8

Other services offered by Parseq Lab:

Service Description Price

One Codex

United States of America

One Codex provides a web-based data platform for identifying microbes in mixed or isolate samples using state-of-the-art metagenomic algorithms. Our technology delivers powerful and accurate microbial characterization while eliminating the need for locally-housed servers or command-line access.

One Codex empowers microbiologists, epidemiologists, and clinical researchers to access the wealth of data provided by modern genome sequencing technology.

Other services offered by One Codex:

Service Description Price
Microbiome Analysis One Codex provides a web-based data platform for identifying microbes in mixed or isolate samples using state-of-the-art metagenomic algorithms. Our technology delivers powerful and accurate microbial characterization while eliminating the need for locally-housed servers or command-line access. Inquire
Metagenomic Analysis One Codex provides a web-based data platform for identifying microbes in mixed or isolate samples using state-of-the-art metagenomic algorithms. Our technology delivers powerful and accurate microbial characterization while eliminating the need for locally-housed servers or command-line access. Inquire

All Genomics

NGS provider Chile

All Genomics is the first Chilean company dedicated to developing genetic tests using the latest technologies for DNA analysis (Next-Generation Sequencing). Our main goal is to develop clinical diagnostic kits validated for Chile and Latin America, with a focus on metabolic diseases. Available kits: - Human microbiome and interpretation - Mitochindrial DNA sequencing and SNP analysis - Pharmacogenomics and SNP analysis - SNP genotyping - Rare diseases investigation - Exome sequencing - Whole genome sequencing

  • Custom panels

  • Animal metagenome and analysis

  • Fungi metagenome
Years in service: 5

Other services offered by All Genomics:

Service Description Price
Microbiome Analysis The report will include main results, bacterial composition from phylum to genus (specie when posible), alpha diversity (family, genus, species and rarefaction curves), beta diversity (family, genus, species and rarefaction curves), Krona visualization template, OTU (family, genus, species). $100.00 USD (per sample)

CosmosID

United States of America

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: 11

Other 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

UConn CORE MARS

NGS provider United States of America

We are a microbiome, amplicon, and genome sequencing facility. We offer services from DNA extraction to library prep (including custom library design) and sequencing.

Years in service: 5

Other services offered by UConn CORE MARS:

Service Description Price
Microbiome Analysis OTU clustering using mothur. Data input fastq, data products: OTU tables for each level, alpha and beta diversity calculations for each level. $150.00 USD (flat price)
Microbiome Analysis Custom statistical analysis of microbiome data. Data input: OTU table, spreadsheets linking sequences with experimental conditions/results. Data output: custom analysis, publication quality figures, etc. Please contact mars@uconn.edu to discuss your needs and to request a quote. $115.00 USD (per hour)

Leucine Rich Bio

India

Other services offered by Leucine Rich Bio:

Service Description Price
Read Filtering and Cleaning Leucine Rich Bio offers Read filtering, cleaning and quality control analysis. We also offer statistical and heuristic analysis. Literature mining services are also provided. As we are Bangalore (India) based company, we offer very competitive pricing. $75.00 USD (per sample)
Transcriptome Annotation Inquire
Small RNA Annotation Inquire
Transcriptome Mapping Inquire
Comparative Genome Analysis Inquire
Variant Annotation Inquire
Differential Gene Expression Analysis Inquire
Targeted Capture Analysis Inquire
SNP / Indel Calling Inquire
SNP / Indel Mapping Inquire
Transcriptome de novo Assembly Inquire
Exome Analysis Inquire
Whole Genome de novo Assembly Inquire
SNP/SV/CNV Discovery Inquire
Custom scripting and special projects Inquire
Genome Annotation Inquire
Genome Mapping Inquire
ChIP-Seq Analysis Inquire
Metagenomic Analysis Inquire
Microbiome Analysis Inquire

DREAMgenics

NGS provider Spain

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

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

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

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

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

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

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

Years in service: 8

Other services offered by DREAMgenics:

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

Microbiome Insights Inc

NGS provider Canada

Microbiome Insights provides pre- and post- consultations (end-to-end services) which include study design and sample guidance on the front end, and bioinformatics consultation on the back end. We offer iTag amplicon sequencing (16S V4, 16S V1-V3 and 16S V4_skin as well as ITS2,18S V4 and Archaeal 16S V4) using the Illumina Miseq, shotgun metagenomics using the Illumina Nextseq or HiSeq, custom qPCR development, SCFA analysis and Calprotectin analysis. We provide our customers with a highly comprehensive, publication quality bioinformatics report. Our depth of expertise allows us to work with various sample types from human, animal, plant, soil and environmental ecosystems.

Other services offered by Microbiome Insights Inc:

Service Description Price
Microbiome Analysis HIghly comprehensive bioinformatics reporting - basic bioinformatics included in price. Additional advanced analytics charges separately. Reporting on amplicon sequencing includes relative abundance and alpha/beta diversity scores. Reporting for shotgun is on a per study basis. Inquire

genexa Ltd

Switzerland

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: 5

Other services offered by genexa Ltd:

Service Description Price
Comparative Genome Analysis Inquire
Microbiome Analysis Inquire
Variant Annotation Inquire
Genome Annotation Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
Custom scripting and special projects Inquire
Whole Genome de novo Assembly 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 Technologie... Inquire
Transcriptome Annotation Inquire
Base Calling Inquire
Differential Gene Expression Analysis Inquire

TACGenomics

United States of America

TACGenomics has a team composed of bioinformatician, molecular biologist and computer scientist who are all at Ph.D. level. Our team has the experience of hundreds of NGS data analysis projects from all over the world. The mission of TACGenomics is to help our customer to solve the biological questions. After computation analysis completed by the bioinformatician, our molecular biologist will interpret the analyzed data carefully, provide more insight into your project and help the publication of the project in the high impact journal.

Years in service: 5

Other services offered by TACGenomics:

Service Description Price
Differential Gene Expression Analysis Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was used to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis. $50.00 USD (per sample)
Transcriptome Mapping The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. TMM (trimmed mean of M-values) was used to normalize the gene expression. $50.00 USD (per sample)
Custom scripting and special projects $50.00 USD (per hour)
Exome Analysis Our team has successfully discovered a causal variant which lead to a mendelian disorder through analyzing 20 samples in three-generation family. The error rate of genotype we called in this family is only 0.2% which indicate that our pipeline detect all the SNV very accurately. $80.00 USD (per sample)
ChIP-Seq Analysis $80.00 USD (per sample)
Genome Mapping $50.00 USD (per sample)
Metagenomic Analysis $100.00 USD (per sample)
Methylation Analysis $100.00 USD (per sample)
Transcriptome de novo Assembly $100.00 USD (per sample)
Whole Genome de novo Assembly $1000.00 USD (per sample)
Microbiome Analysis $50.00 USD (per sample)