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:

Databases

MetaMLST automatically downloads the latest version of its database. You can also manually download databases from here. The latest database is: metamlstDB_2022.

Publication

• Moreno Zolfo, Adrian Tett, Olivier Jousson, Claudio Donati and Nicola Segata - MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples - Nucleic Acids Research, 2016 DOI: 10.1093/nar/gkw837

Where can I get support?

• Bugs and Support: MetaMLST Users Support Group
• Project page at SegataLab
• Project Wiki