bcbio/bcbio-nextgen: (original) (raw)

Published December 15, 2021 | Version v1.2.9

Software Open

Creators

• Brad Chapman1

• Rory Kirchner2

• Lorena Pantano3

• Sergey Naumenko

• Matthias De Smet4

• Luca Beltrame

• Tetiana Khotiainsteva

• Ilya Sytchev5

• Roman Valls Guimera6

• John Kern

• Christian Brueffer7

• Vlad Savelyev8

• Guillermo Carrasco9

• Mario Giovacchini10

• Miika Ahdesmaki11

• Paul Tang12

• Sehrish Kanwal13

• James J Porter14

• Steffen Möller15

• Vang Le16

• Alexandru Coman17

• bogdang989

• Valentine Svensson18

• Brent Pedersen19

• Jeff Hammerbacher

• Matt Edwards

• Meeta Mistry20

• apastore

• Peter Cock

• Joon Yoon

• 1. Ginkgo Bioworks

• 2. Patch Biosciences

• 3. Harvard Chan School of Public Health

• 4. @CenterForMedicalGeneticsGhent

• 5. @hsph-qbrc @onnela-lab

• 6. University of Melbourne

• 7. SAGA Diagnostics / Lund University

• 8. @populationgenomics

• 9. @iZettle

• 10. Science for Life Laboratory

• 11. AstraZeneca

• 12. startup

• 13. The University of Melbourne

• 14. Recurse Center

• 15. University of Rostock

• 16. Aalborg University

• 17. @tss-yonder

• 18. Serqet Therapeutics

• 19. University of Utrecht

• 20. HSPH

Description

• 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

bcbio/bcbio-nextgen-v1.2.9.zip

Files (17.8 MB)

Additional details