Difference between revisions of "MentaLiST"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
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Revision as of 21:21, 6 December 2019
Description
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying strain types from a set of a small number of housekeeping genes. With the increased availability of whole-genome sequencing (WGS) data, MLST methods have evolved toward larger typing schemes, based on a few hundred genes (core genome MLST, cgMLST) to a few thousand genes (whole genome MLST, wgMLST). Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large cgMLST and wgMLST schemes.
Required Modules
Serial
- gcc/5.2.0
- mentalist
System Variables
- HPC_MENTALIST_DIR - installation directory
- HPC_MENTALIST_BIN - executable directory