A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses.
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.
Platt
S
S
Statistics, Modelling and Bioinformatics Group, Health Protection Agency, Centre for Infections, London, UK. steven.platt@hpa.org.uk
Pichon
B
B
George
R
R
Green
J
J
D001419:Bacteria / Q000145:classification* / Q000235:genetics; D015373:Bacterial Typing Techniques / Q000379:methods*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D001330:Electronic Data Processing; D017421:Sequence Analysis
D004269:DNA, Bacterial