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SRST2 v0.1.3 - Short Read Sequence Typing for Bacterial Pathogens
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@katholt katholt released this 07 Feb 01:20
· 198 commits to master since this release
v0.1.3a
3355138

Updates in this release

  • fixed a bug that occurred while trying to type genes from a user-supplied database (see issue #5, thanks to Scott Long)
  • fixed a bug in gene detection reporting - genes are now correctly reported by cluster, rather than by gene symbol (see issue #7)
  • added maximum divergence option for reporting, default is now to report only hits with <10% divergence from the database (see issue #8)
  • added parameter to pass to bowtie2 parameter '-u N' to stop mapping after the first N reads. Default behaviour remains to map all reads. However, for large read sets (e.g. >100x), extra reads do not help and merely increase the time taken for mapping and scoring, and you may want to limit to the first million reads (100x of a 2 Mbp genome) using '--stop_after 1000000'.
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