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Metagenomic sequencing software tools

High-throughput sequencing software tools

Metagenomic sequencing applications

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Metagenomic sequencing 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., 1998). Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Due to the differences between the metagenomic data obtained from whole genome sequencing and amplicon sequencing methods, there are significant differences between the corresponding bioinformatics tools for these data.

Most Recent Tools

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OMIC_12638
Data visualization

Metagenomics Core Microbiome Exploration Tool
MetaCoMET

A web platform that enables the discovery and visualization of the core microbiome and…

A web platform that enables the discovery and visualization of the core microbiome and provides a comparison of the relative abundance and diversity patterns between subsets of samples within a microbiome dataset. MetaCoMET provides an efficient and…

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OMIC_12611
Interpretation

RevEcoR

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

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 large-scale ecological insights into species’ ecology…

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OMIC_12606
Functional annotation

Qnr-search

A method to detect and annotate novel classes of qnr antibiotic resistance genes in…

A method to detect and annotate novel classes of qnr antibiotic resistance genes in nucleotide sequence data. Qnr-search uses a hidden Markov model with a fragment length-dependent classification rule and has a high sensitivity and specificity, even…

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OMIC_12578
Taxonomy-dependent

PhyloPythiaS+
PPS+

A taxonomic assignment program that produces accurate assignments with a precision of 80%…

A taxonomic assignment program that produces accurate assignments with a precision of 80% or more also for low-ranking taxa from metagenome samples. PPS+ is a fully automated successor of the PhyloPythiaS software. It automatically determines the…

Most Popular Tools

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OMIC_00653
Fragment recruitment

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads)…

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 Burrows-Wheeler index to keep its memory footprint…

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OMIC_01499
Data visualization

MetaSee

An online toolbox for metagenomic data visualization.

An online toolbox for metagenomic data visualization.

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OMIC_03698
Metagenomic assembly

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 data analysis. Enabling microbiology researchers to…

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OMIC_01306
Differential abundant features

DESeq2

A method for differential analysis of count data, using shrinkage estimation for…

A method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the…

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