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SRST2 v0.2.0 - Short Read Sequence Typing for Bacterial Pathogens

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@rrwick rrwick released this 30 Jul 05:18
· 52 commits to master since this release
v0.2.0
f50e476

Updates in v0.2.0

  1. Some improvements to allele calling, particularly for Klebsiella MLST locus mdh, kindly contributed by andreyto. Includes rejection of read alignments that are clipped on both ends (likely to be spurious) and minor bug fixes associated with depth calculations.
  2. Updated E. coli serotype database to remove duplicate sequences.
  3. Added mcr-2 colistin resistance gene to ARGannot.r1.fasta resistance gene database.
  4. A --threads option was added, which makes SRST2 call Bowtie and Samtools with their threading options. The resulting speed up is mostly due to the Bowtie mapping step which parallelises very well.
  5. The VFDB_cdhit_to_csv.py script was updated to work with the new VFDB FASTA format.
  6. Versions of Bowtie2 up to 2.2.9 are now supported. Samtools v1.3 can now be used as well, however v0.1.18 is still the recommended version (for reasons discussed below).
  7. Added scripts/qsub_srst2.py to generate SRST2 jobs for the Grid Engine (qsub) scheduling system (http://gridscheduler.sourceforge.net/). Thanks to Ramon Fallon from the University of St Andrews for putting this together. Some of the specifics are set up for his cluster, so modifications may be necessary to make it run properly on a different cluster using Grid Engine.
  8. Various other small bug fixes!
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