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2.11.1
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@d-cameron d-cameron released this 30 Mar 23:38
· 158 commits to master since this release
v2.11.1
b6342f9

Bug fixes and a VIRUSBreakend database updates.

  • Added bacteria and archaea to VIRUSBreakend db
    • Fixes false positives caused by bacteria reads with short homology to viral genomes in the expanded viral database
    • VIRUSBreakend database must be rebuilt.
    • If you haven't deleted the kraken2 intermediate files, the rebuild can be done by running just the following steps:
      • kraken2-build --download-library bacteria --db $dbname
      • kraken2-build --download-library archaea--db $dbname
      • kraken2-build --threads $(nproc) --build --db $dbname
      • tar -czvf virusbreakend.db.$dbname.tar.gz $dbname/*.k2d $dbname/taxonomy/nodes.dmp $dbname/library/viral/*.fna* $dbname/library/added/*.fna* $dbname/taxid10239.nbr $dbname/seqid2taxid.map
  • #474 #476 Fixed off-by-one crash error occurring when read length was an exact multiple of 32.
  • #475 Fixed --externalaligner handling
  • #480 Aborting VIRUSBreakend upon gridsstools failure
  • #480 clarified VIRUSBreakend gridsstools error message
  • #478 Added defensive check to NonReferenceContigAssembler.SupportLookup
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