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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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Concordance/Contamination of paired samples

OMIC_12429
Sequence contamination…

Concordance/Contamination of paired samples
Conpair

A tool for detection of sample swaps and cross-individual contamination in whole-genome…

A tool for detection of sample swaps and cross-individual contamination in whole-genome and whole-exome tumor–normal sequencing experiments. Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance…

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Comparative weighted Venn Tree

OMIC_12363
Data visualization

Comparative weighted Venn Tree
CoVennTree

Simultaneously compares up to three multifarious datasets by aggregating and propagating…

Simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. The underlying concept of CoVennTree is to bring information from the…

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Vecuum

OMIC_12231
Sequence contamination…

Vecuum

A Java based variant caller designed for detecting contamination-induced point mutations…

A Java based variant caller designed for detecting contamination-induced point mutations from hybrid-capture-based genome sequencing data (WGS, WES, targeted capture, etc). Vecuum is specialized for identifying false variants caused by recombinant…

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Centrifuge

OMIC_12217
Taxonomy-dependent

Centrifuge

A rapid and sensitive classifier for microbial sequences with low memory requirements and…

A rapid and sensitive classifier for microbial sequences with low memory requirements and a speed comparable to the fastest systems. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM)…

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