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SRST2 v0.1.8 - Short Read Sequence Typing for Bacterial Pathogens
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@katholt katholt released this 15 Mar 02:57
· 93 commits to master since this release
v0.1.8
e30dd01

Updates in v0.1.8

/data directory includes files for subtyping of the LEE pathogenicity island of E. coli, as per Ingle et al, 2016, Nature Microbiology. Instructions below

Resistance gene database updates:

Fixed ARGannot.r1.fasta to include proper mcr1 DNA sequence.
Added columns to the ARGannot_clustered80.csv table, to indicate classes of beta-lactamases included in the ARGannot.r1.fasta database according to the NCBI beta-lactamase resource (new location for the Lahey list).

Fixed some issues with handling of missing data (i.e. where there were no hits to MLST and/or no hits to genes) when compiling results into a table via --prev_output. This could result in misalignment of gene columns in previous versions.

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