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

Shotgun metagenomic sequencing data analysis bioinformatics software tools

Most Recent Tools

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VALET
Desktop

VALET VALidating mETagenomic assemblies

Allows to perform de novo validation of metagenomic assemblies. VALET verifies…

Allows to perform de novo validation of metagenomic assemblies. VALET verifies a number of properties that should hold true for a correct assembly. If invariants are incorrect, they are reported one…

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MetaSort
Desktop

MetaSort

Recovers nearly complete genomes from metagenomic samples. MetaSort combines…

Recovers nearly complete genomes from metagenomic samples. MetaSort combines the advantages of traditional metagenomics and single-cell genomics. It is able to segregate small subsets of cells with…

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PHYSCIMM
Desktop

PHYSCIMM PHY Sequence Clustering with Interpolated Markov Models

Allows to model clusters of sequences. PHYSCIMM uses interpolated Markov models…

Allows to model clusters of sequences. PHYSCIMM uses interpolated Markov models (IMMs). It was tested by clustering sequencing reads from an in vitro-simulated microbial community. The tool…

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LikelyBin
Desktop

LikelyBin

Allows to cluster sequences with high accuracy. LikelyBin is based on k-mer…

Allows to cluster sequences with high accuracy. LikelyBin is based on k-mer distributions and uses a Markov Chain Monte Carlo (MCMC) framework. It estimates the set of master distributions and…

Most Popular Tools

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Bowtie
Desktop

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA…

An ultrafast, memory-efficient short read aligner. It 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…

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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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