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MetaMLST

A computational pipeline for MLST typing from metagenomic data

MetaMLST performs an in-silico Multi Locus Sequence Typing (MLST) Analysis on metagenomic samples, directly from raw reads. MetaMLST achieves cultivation- and assembly- free strain level tracking and profiles all the species to which the standard MLST protocol is applicable.

Current database version: [ May 2022 ]

What can I use MetaMLST for?

  • Strain-level identification
  • Microbial population analysis

How can I use it?

This repo contains sub-repositories, to clone it use:

git clone --recurse-submodules https://github.com/SegataLab/metamlst.git

Check out the Quick Start or refer to the Wiki for the documentation. You can also try the examples, or take a look to the Examples section

How it works?

MetaMLST reconsctructs the MLST loci-sequences using the closest reference from the publicly available datsets (PubMLST) and traces the most abundant strain of each species: MetaMLST pipeline schema

Databases

MetaMLST automatically downloads the latest version of its database. You can also manually download databases from here. The latest database is: metamlstDB_2021.

Publication

Where can I get support?

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MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.

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