Shotgun metagenomic sequencing data analysis bioinformatics software tools

Metagenomic sequencing analysis steps

Metagenomic sequencing analysis workflow

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Metagenomic sequencing analysis workflow schema
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.,…

Shotgun metagenomic sequencing data analysis bioinformatics software tools

Most Recent Tools

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microbeGPS
Desktop

microbeGPS

Identifies microbial organisms in metagenomic sequencing data, estimates their…

Identifies microbial organisms in metagenomic sequencing data, estimates their abundance, and quantifies their distances to known reference genomes. MicrobeGPS is a bioinformatics software for the…

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Seqenv
Desktop

Seqenv

Performs similarity searches of short sequences against the ‘‘nt’’…

Performs similarity searches of short sequences against the ‘‘nt’’ nucleotide database provided by NCBI and, out of every hit, extracts the textual metadata field. Seqenv is a software that…

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reference-based…
Desktop

reference-based ribosome assembly

Integrates taxonomic tree search and Dirichlet process clustering to…

Integrates taxonomic tree search and Dirichlet process clustering to reconstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy. RAMBL realizes the access to…

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MetaShot
Desktop

MetaShot Metagenomics Shotgun

Assesses the total microbiome composition from host-associated shotgun sequence…

Assesses the total microbiome composition from host-associated shotgun sequence data. MetaShot shows its overall optimal accuracy performance by analyzing both simulated and real datasets. It…

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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