mICROBIOMICs tools

mOTUs

Official website: https://motu-tool.org/

Github: https://github.com/motu-tool/mOTUs

Papers:
Description: mOTUs is a command line tool design for taxonomic profiling of metagenomic samples. mOTUs allow to identify known and currently unknown species using a set of 10 universal single copy marker genes. The input is a metagenomic sample (represented as one or more fastq file) and the output is a taxonomic profile which identify which species are present and their relative abundance.

Graphical abstract: mOTUs
mTAGs

Github: https://github.com/SushiLab/mTAGs

Paper: Salazar, Ruscheweyh et al. Bioinformatics 2021

Description: mTAGs is a tool for the taxonomic profiling of metagenomes. It detects sequencing reads belonging to the small subunit of the ribosomal RNA (SSU-rRNA) gene and annotates them through the alignment to full-length degenerate consensus SSU-rRNA reference sequences. The tool is capable of processing single-end and pair-end metagenomic reads, takes advantage of the information contained in any region of the SSU-rRNA gene and provides relative abundance profiles at multiple taxonomic ranks, including OTUs defined at a 97% sequence identity cutoff. Although the primary use of mTAGs is the taxonomic profiling of metagenomes, it can also be used for profiling SSU-rRNA amplicon data or for classifying amplicon sequence variants.

Graphical abstract: mTAGs_abstract
mVIRs

Github: https://github.com/SushiLab/mVIRs

Paper: Z√ľnd et al. Microbiome 2021

Description: VIRs is a bioinformatics tool to locate the integration sites of inducible mobile genetic elements, mainly prophages, in microbial genomes. It exclusively identifies prophages found in circularised or concatena ted form after the induction. The prophages are detected by analysing the orientation and apparent insert size of paired-end reads aligned to a reference genome and locates the exact genomic coordinates by partially aligned reads. mVIRs a pplies to microbial community samples, using either publicly available or de novo assembled genomes as references for the alignment of sequencing reads. The output of mVIRs can be quality checked and annotated by tools, such as checkV or VirSorter2 and PHANOTATE, to identify putative prophage candidates and builds the foundation to quantify phage-to-host ratio as relative prophage activity levels.

Graphical abstract: mVIRs_abstract