Difference between revisions of "Mlstcheck"

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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|mlstcheck}} |{{#vardefine:url|https://github.com/sanger-pathogens/mlst_check...")
 
 
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 22:43, 8 September 2020

Description

mlstcheck website  

This application is for taking MLST databases from multiple locations and consolidating them in one place so that they can be easily used (and kept up to date). Then you can provide FASTA files and get out sequence types (ST) for a given MLST database. Two spreadsheets are outputted, one contains the allele number for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele. If more than 1 allele gives 100% identity for a locus, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, unseen alleles are saved in FASTA format, with 1 per file, for submission to back to MLST databases.

Environment Modules

Run module spider mlstcheck to find out what environment modules are available for this application.

System Variables

  • HPC_MLSTCHECK_DIR - installation directory
  • HPC_MLSTCHECK_BIN - executable directory




Citation

If you publish research that uses mlstcheck you have to cite it as follows:

"Multilocus sequence typing by blast from de novo assemblies against PubMLST", Andrew J. Page, Ben Taylor, Jacqueline A. Keane, The Journal of Open Source Software, (2016).