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 14)


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, 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: 10

Other services offered by Applied Biological Materials Inc.:

Service Description Price

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: 13

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
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
Microbiome Analysis We provide 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

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: 15

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

CD Genomics

NGS provider United States of America

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: 19

Other services offered by CD Genomics:

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

Leucine Rich Bio

India

Leveraging the expanding prospects of microbiome research, Leucine Rich Bion has integrated a robust computational pipeline "MetaRich" into a user-friendlyplatform for comprehensive analyses of any microbiome data.

After rigorous testing & validation of several leading microbiome analysis pipelines, tools & databases, we have compiled “MetaRich” to analyze both 16s rDNA & shotgun metagenomes, duly supplemented by our in-house computational tools. MetaRich will assist both researchers & industry personnel who are in pursuit of discovering biological insights within complex microbial systems & will ease the arduous task of large-scale microbiome data analysis.

Years in service: 10

Other services offered by Leucine Rich Bio:

Service Description Price
Microbiome Analysis For Individual Samples Abundance data - Raw & % Normalized Abundance Bar plots - Raw & % Normalized Pie charts - Kingdom through Phylum Alpha diversity Plots & index value table AMR Prediction Comparative Analyses Differential abundance data (across groups) Abundance Bar plots Raw & % Normalized Alpha diversity Plots & index value table Beta diversity Plots & index value table PCoA analysis & pl… $9.00 USD (per sample)

Dreamgenics

NGS provider Spain

Dreamgenics is a biotech company that offers bioinformatics analysis services for genomic, transcriptomic and metagenomic NGS data using our Genome One software. Genome One (CE-IVD certified) is an advanced tool that allows the integration of all the bioinformatics solutions required for the study, including read alignment, variant calling and annotation. Our analyses identify high-quality genomic variants through high sensitivity and specificity standards, extracting important biological information and reducing validation costs. The services that we offer are the following: WGS, WES, Gene panels, Transcriptomics (RNA-Seq) and Metagenomics. Additionally, we hand in the results using our web viewer Genome One Reports (https://www.dreamgenics.com/en/genome-one/).

The use of our bioinformatics tools allows us to offer you high-quality results in a fast and simple way. By using our analysis services, you considerably reduce costs and the investment in technological devices, informatics and qualified professionals.

Lastly, we are an ISO 9001:2015, UNE-EN ISO 13485:2018 and UNE-ISO/IEC 27001:2017 certified company which represents our commitment to provide our customers with products and services that meet the most demanding quality standards.

Years in service: 12

Other services offered by Dreamgenics:

Service Description Price
Single Cell RNA-Seq Analysis We offer Single cell RNA-Seq bioinformatic analysis from FASTQ files including: - Sequencing and mapping quality control. - Alignment of reads against reference genome. - Quantification of gene expression at the single cell level. - Reduction of data dimensionality. - Clustering or division of cells into different groups and subgroups. - Differential gene expression analysis. - Study of the evol… $200.00 USD (per sample)
Differential Gene Expression Analysis Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)
Exome Analysis Our bioinformatics analysis includes: Quality control, Alignment, Detection of high quality variants (SNVs, translocations and CNVs), Filtering of common variants, Annotation of variants obtained with multiple databases and prediction algorithms and Comparison between samples and extraction of recurrent variants. We will deliver the results to the Genohub data bucket as well as through our platf… $80.00 USD (per sample)
Transcriptome Annotation Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)

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: 10

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. $115.00 USD (per hour)

Igenbio, Inc.

United States of America

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: 11

Other services offered by Igenbio, Inc.:

Service Description Price
Differential Gene Expression Analysis Inquire
Comparative Genome Analysis Inquire
Metagenomic Analysis - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 and Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva,… Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Gene Annotation and Functional Assignments placing genes into their functional or metabolic context utilizing KEGG Pathways, Gene Ontology, and the ERGO database. Optional - Identification of Antibiotic Resistance - including the genes, pathways, and specific drugs Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly All current sequencing technologies support - Illumina, PacBio, Oxford Nanopore, 10x, Hi-C, Ion Torrent, and others. Igenbio scientists utilize a multitude of assembly strategies - denovo, reference based, hybrid, metagenomic, and others. Inquire
Base Calling Inquire
Microbiome Analysis - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 or Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva, Gree… Inquire

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, ITS2,18S V4) using the Illumina Miseq, shotgun metagenomics and shallow shotgun using the Illumina Nextseq, custom qPCR development, and SCFA 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.

Years in service: 9

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: 9

Other services offered by genexa Ltd:

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

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: 9

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)

EarlyDx

NGS provider

EarlyDx is committed to providing cutting-edge non-invasive genomics technologies and best-in-class early disease diagnostics. Our proprietary cfDNA-based technologies, in combination with powerful AI algorithms, have shown great potential to transform non-invasive biomarker discovery, diagnostics, and precision medicine for almost any diseases, including cancers, aging, metabolic diseases, autoimmune diseases, imprinting diseases, and neurological diseases.

Our key cfDNA-based best-in-class technologies include:

  1. cfMethyl-seq: a powerful and cost-effective NGS solution to profile the cfDNA methylome
  2. cfSNV: a cutting-edge computational tool to accurately call mutations directly from blood
  3. cfTrack: for non-invasive monitoring of cancer MRD, recurrence, and evolution
  4. EarlyDx-Cloud: a comprehensive bioinformatics data analysis platform for liquid biopsy

Please check out our relevant publications in details: https://earlydx.com/technologies/publications/

Years in service: 2

Other services offered by EarlyDx:

Service Description Price

Center for Bioinformatics and Functional Genomics

NGS provider United States of America

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: 10

Other services offered by Center for Bioinformatics and Functional Genomics:

Service Description Price
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)
Custom scripting and special projects Contact us about the possibility of a custom project/scripting for your problem. Inquire
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)
Transcriptome Annotation Full transcriptome annotation via NCBI BlastX nr database, PFAM, and KEGG Pathways mapping. $300.00 USD (flat price)
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)