Shotgun metagenomic sequencing data analysis bioinformatics software tools

Metagenomics is defined as the study of the metagenome, which is total genomic DNA from environmental samples. Metagenomics has long been one of the major research tools in microbial ecology since the term was first used in 1998 (Handelsman et al., 1998). Metagenomics has become…

Metagenomic sequencing analysis steps

Metagenomic sequencing analysis workflow

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Metagenomic sequencing analysis workflow schema

Most recent bioinformatics tools

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lattice-metage
Desktop

lattice-metage

Allows clustering of metagenomic datasets. lattice-metage is a two-dimensional…

Allows clustering of metagenomic datasets. lattice-metage is a two-dimensional lattice model that can incorporate information from multiple models. The software backs-off to a combination of multiple…

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MetaGen
Desktop

MetaGen

Offers a reference-free metagenomic binning method for identifying bacteria…

Offers a reference-free metagenomic binning method for identifying bacteria species and quantifying their distribution. MetaGen clusters short contigs for samples with low coverage and distinguish…

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FastViromeExplo…
Desktop

FastViromeExplorer

Identifies and quantifies the abundance of viruses in metagenomics data.…

Identifies and quantifies the abundance of viruses in metagenomics data. FastViromeExplorer is a stand-alone pipeline that uses kallisto to map short reads to a reference virus database and then…

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MetaComp
Desktop

MetaComp

Allows comparison of metagenomics and other meta-omics data. MetaComp is a…

Allows comparison of metagenomics and other meta-omics data. MetaComp is a graphical software that incorporates metagenomics, metatranscriptomics, metaproteomics and metabolomics data. The software…

Most popular analytical software

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

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MetaSee
Web

MetaSee

An extendable toolbox to facilitate the interactive visualization of…

An extendable toolbox to facilitate the interactive visualization of metagenomic samples of interests. MetaSee includes: (I) a core visualization engine that is composed of different views for…

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QIIME
Desktop

QIIME Quantitative Insights Into Microbial Ecology

An open source software package for comparison and analysis of microbial…

An open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data.

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Orione
Web

Orione

A Galaxy-based framework consisting of publicly available research software and…

A Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology…

Curators for Metagenomic sequencing analysis

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