A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses

Steven Platt*, B. Pichon, R. George, J. Green

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.

Original languageEnglish
Pages (from-to)1144-1146
Number of pages3
JournalClinical Microbiology and Infection
Issue number11
Publication statusPublished - Nov 2006

Bibliographical note

Funding Information:
Some aspects of this work were funded by the Department of Health, UK. The authors would like to acknowledge Applied Maths (Sint-Martens-Latem, Belgium) for providing the core functionality of the script to assign allelic profiles. The MLST pipeline is fully functional on BioNumerics v.4.0 or later. The scripts that enable the pipeline, plus guidelines and installation instructions, are available from the authors on request.


  • Analysis
  • DNA sequence editing
  • Datafiles
  • Multilocus sequence typing
  • Sequencing
  • Typing


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