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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_12805
Workflows & pipelines

Illinois Mayo Taxon Organization from RNA Dataset Operations
IM-TORNADO

A workflow for processing non-overlapping reads while retaining maximal information…

A workflow for processing non-overlapping reads while retaining maximal information content. IM-TORNADO is used for carrying out common microbiome analyses leveraging the information of the paired reads provided by the Illumina sequencers to relate…

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OMIC_12720
Protein database search

SW#db

A parallelised version of exact database search algorithms optimised for multiple…

A parallelised version of exact database search algorithms optimised for multiple queries. Although the emphasis is on the Smith-Waterman algorithm, other exact algorithms such as global and semi-global alignment are provided as well. SW#db is…

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OMIC_12719
Protein database search

Smith Waterman On Reduced Database
SWORD

A heuristic tool for protein database search which combines a heuristic and an exact…

A heuristic tool for protein database search which combines a heuristic and an exact approach. It is aimed to replace BLAST, as it is faster between 8 and 16 times and has better or comparable sensitivity. The second main advantage is that it…

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OMIC_12713
16S rRNA reconstruction

Expectation-Maximization Iterative Reconstruction of Genes from the…
EMIRGE

Reconstructs full-length small subunit (SSU) sequences from metagenomic data from a…

Reconstructs full-length small subunit (SSU) sequences from metagenomic data from a microbial community of interest, accurate to the species level. In addition, the method also provides accurate SSU sequence abundance estimates. EMIRGE is robust to…

Most Popular Tools

popular
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…

popular
OMIC_01499
Data visualization

MetaSee

An online toolbox for metagenomic data visualization.

An online toolbox for metagenomic data visualization.

popular
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…

popular
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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