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2.10.2
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@d-cameron d-cameron released this 10 Dec 05:01
· 267 commits to master since this release
v2.10.2
36c5c21
  • Added support for batched assembly #354 #397 #403 #406 #430
  • Overhaul of VIRUSBreakend behaviour
    • Added a OUTPUT.summary.csv file that is always written
      • This file is only written if VIRUSBreakend was successful
      • Provides useful stats such as viral presence, coverage, and number of integrations found
    • increased assembly threshold cut-offs
      • Better integration detection on samples with high (1000x+) viral coverage
    • Removed Virus-Host DB dependency due to Non-Commerical licence restriction
      • Now determining human virus status from NCBI virus host file
      • This change requires a rebuild of the VIRUSBreakend database
    • Maximum of 1 virus reported per genus
      • Stops multiple viral strains/subtypes being reporting due to a small portion of reads being misclassified by kraken2
  • Added scripts for reproduction of results in VIRUSBreakend manuscript
  • Fixed crash bug in VirusBreakendFilter
  • Added kraken version to VIRUSBreakend output
  • Added check for existence of RepeatMasker
  • BEALN now always replaces pipes in contig name with underscores
  • Removed unnecessary GKL library warning message
  • Hard limit maximum assembly base quality to the max of 93 representable by Sanger format fastq #404
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