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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COMMET
Desktop

COMMET COmpare Multiple METagenomes

Provides a global similarity overview between all datasets of a metagenomic…

Provides a global similarity overview between all datasets of a metagenomic project. COMMET is able to (1) filter reads, given user-defined parameters, (2) compare all-against-all read sets, and (3)…

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Consensus…
Desktop

Consensus Sequence Searches

Allows users to search and align databases of consensus sequences. ConSequenceS…

Allows users to search and align databases of consensus sequences. ConSequenceS is a method for consensus sequence-based comparisons that improves searches and alignments as an add-on to PSI-BLAST.

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MGS Canopy…
Desktop

MGS Canopy Algorithm

Enables comprehensive discovery of new microbial organisms, viruses and…

Enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities. MGS Canopy Algorithm aids to assembly microbial genomes without the need for reference…

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PhytoREF
Dataset

PhytoREF

Explores, evaluates and monitors the diversity of photosynthetic eukaryotes in…

Explores, evaluates and monitors the diversity of photosynthetic eukaryotes in aquatic and terrestrial ecosystems. PhytoREF is a database built through the compilation of all of the publicly…

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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