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Decision-support software tools | Shotgun metagenomic sequencing data analysis

Interpretation of the metagenomic data plays a central role in projects aiming to explore the most essential questions in microbiology, namely ‘In a given environment, among the microbes present, what are they doing, and how are they doing…
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MEGAN
Desktop

MEGAN MEtaGenome ANalyzer

Allows to interactively explore and analyze, both taxonomically and…

Allows to interactively explore and analyze, both taxonomically and functionally, large-scale microbiome sequencing data. MEGAN is a comprehensive microbiome analysis toolbox for metagenome,…

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InterProScan
Desktop
Web

InterProScan

Scans sequences against InterPro's signatures. InterProScan allows users…

Scans sequences against InterPro's signatures. InterProScan allows users to characterize a nucleotide or protein function by matching it with models from several different databases and to…

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HUMAnN
Desktop

HUMAnN The HMP Unified Metabolic Analysis Network

A pipeline for efficiently and accurately determining the presence/absence and…

A pipeline for efficiently and accurately determining the presence/absence and abundance of microbial pathways in a community from metagenomic data.

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CoMet
Web

CoMet

Offers search options for the identification of peptides and proteins in…

Offers search options for the identification of peptides and proteins in proteomics experiments. Comet implements the fast cross-correlation algorithm to score peptide sequences against experimental…

MG-RAST
Dataset

MG-RAST

An open-submission data portal for processing, analyzing, sharing and…

An open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of…

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BugBase
Web
Desktop

BugBase

Leverages pre-existing databases, annotations and frameworks, along with manual…

Leverages pre-existing databases, annotations and frameworks, along with manual curation. BugBase is an algorithm with a user-friendly graphical user interface (GUI) for analyzing microbiome data…

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SmashCommunity
Desktop

SmashCommunity

A stand-alone metagenomic annotation and analysis pipeline suitable for data…

A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies.

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RevEcoR
Desktop

RevEcoR

An R package and a Shiny Web application that implements the reverse ecology…

An R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe–microbe interactions in microbial communities. RevEcoR allows users to obtain…

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MUSiCC
Desktop
Web

MUSiCC

A software package for normalizing and correcting gene abundance measurements…

A software package for normalizing and correcting gene abundance measurements derived from metagenomic shotgun sequencing. For intra-sample gene normalization, it uses a set of genes that are…

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RAMMCAP
Desktop

RAMMCAP

Analysis and comparison of very large metagenomes with fast clustering and…

Analysis and comparison of very large metagenomes with fast clustering and functional annotation.

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Interpro2GO
Desktop

Interpro2GO

Classifies sequences into protein families and predicts the presence of…

Classifies sequences into protein families and predicts the presence of important domains and sites. InterPro is an integrated resource of protein families, domains and sites which are combined from…

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IMNGS
Web

IMNGS Integrated Microbial NGS

Offers a complete workflow for de novo analysis of users’ own raw 16S rRNA…

Offers a complete workflow for de novo analysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS is an innovative platform that uniformly and…

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metaFunction
Desktop

metaFunction

A powerful tool in accurate profiling functions in a metagenomic sample.…

A powerful tool in accurate profiling functions in a metagenomic sample. metaFunction detects all possible functional roles at the low level from a metagenomic sample/community. In the first step a…

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MetaNetSam
Desktop

MetaNetSam Metabolic Network Sampling

A probabilistic sampling approach to profiling metabolic reactions in a…

A probabilistic sampling approach to profiling metabolic reactions in a microbial community from metagenomic shotgun reads, in an attempt to understand the metabolism within a microbial community and…

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RDP Library Compare
Web

RDP Library Compare Ribosomal Database Project Library Compare

Uses the RDP naive Bayesian classifier to provide rapid classification of…

Uses the RDP naive Bayesian classifier to provide rapid classification of library sequences into the new phylogenetically consistent higher-order bacterial taxonomy. RDP Library Compare is an online…

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GOmixer
Web

GOmixer

A user-friendly web application designed to compare, integrate and visualize…

A user-friendly web application designed to compare, integrate and visualize meta-omics data from gut microbial communities (metagenomics, metatranscriptomics, metametabolomics, and metaproteomics)…

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CAMERA
Desktop
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