MentaLiST v0.2.5 – A fast MLST caller for large MLST schemes

MentaLiST v0.2.5

:: DESCRIPTION

MLST (multi-locus Sequence Typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance.

MentaLiST is a new MLST caller, based on a k-mer counting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • conda

:: DOWNLOAD

MentaLiST

:: MORE INFORMATION

Citation

Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L.
MentaLiST – A fast MLST caller for large MLST schemes.
Microb Genom. 2018 Feb;4(2):e000146. doi: 10.1099/mgen.0.000146. Epub 2018 Jan 10. PMID: 29319471; PMCID: PMC5857373.

krocus 0.0.15 – Predict MLST directly from uncorrected long reads

krocus 0.0.15

:: DESCRIPTION

Krocus can predict a ST directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Krocus

:: MORE INFORMATION

Citation

PeerJ. 2018 Jul 31;6:e5233. doi: 10.7717/peerj.5233. eCollection 2018.
Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus.
Page AJ, Keane JA.

SimMLST 1.0 – Simulation of MLST data under a Neutral Model

SimMLST 1.0

:: DESCRIPTION

SimMLST, a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample. Such simulations are useful to make interpretations about real datasets.Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50,000 isolates in over 50 different species and its results are freely available from the pubMLST website.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SimMLST

:: MORE INFORMATION

Citation

Didelot, Lawson and Falush (2009)
SimMLST: simulation of multi-locus sequence typing data under a neutral model
Bioinformatics (2009) 25 (11): 1442-1444.