Software Open Access

bcbio/bcbio-nextgen:

Brad Chapman; Rory Kirchner; Lorena Pantano; Sergey Naumenko; Matthias De Smet; Luca Beltrame; Tetiana Khotiainsteva; Ilya Sytchev; Roman Valls Guimera; John Kern; Christian Brueffer; Vlad Savelyev; Guillermo Carrasco; Mario Giovacchini; Miika Ahdesmaki; Paul Tang; Sehrish Kanwal; James J Porter; Steffen Möller; Vang Le; Alexandru Coman; bogdang989; Valentine Svensson; Brent Pedersen; Jeff Hammerbacher; Matt Edwards; Meeta Mistry; apastore; Peter Cock; Joon Yoon

  • Fix vcf header bug: T/N SAMPLE lines are back - needed for import to SolveBio
  • add strandedness: auto for -l A option in salmon
  • report 10x more peaks in CHIP/ATAC-seq - use 0.05 qvalue
  • fix misleading RNA-seq duplicated reads statistics: thanks @sib-bcf
  • reorganize conda environments
  • snpEff 5.0
  • strandedness: auto
  • document WGBS pipeline steps
  • make --local an option, not default in bismark alignment - too slow
  • bcbioRNASeq update to 0.3.44
  • pureCN update to 2.0.1
  • octopus update to 0.7.4
Files (17.8 MB)
Name Size
bcbio/bcbio-nextgen-v1.2.9.zip
md5:f2f349a21c74b8d62e3283843dcaebae
17.8 MB Download
2,698
175
views
downloads
All versions This version
Views 2,698557
Downloads 17538
Data volume 3.1 GB677.0 MB
Unique views 2,139493
Unique downloads 15237

Share

Cite as