SRST2 v0.1.3 - Short Read Sequence Typing for Bacterial Pathogens
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'.