Published April 14, 2021
| Version v.1.2.8
Software
Open
bcbio/bcbio-nextgen:
Creators
- Brad Chapman1
- Rory Kirchner2
- Lorena Pantano2
- Sergey Naumenko
- Matthias De Smet3
- Luca Beltrame
- Tetiana Khotiainsteva
- Ilya Sytchev4
- Roman Valls Guimera5
- John Kern
- Christian Brueffer6
- Vlad Savelyev7
- Guillermo Carrasco8
- Mario Giovacchini9
- Miika Ahdesmaki10
- Paul Tang11
- Sehrish Kanwal12
- James J Porter13
- Steffen Möller14
- Vang Le15
- Alexandru Coman16
- bogdang989
- Valentine Svensson17
- Brent Pedersen18
- Jeff Hammerbacher19
- Matt Edwards
- Meeta Mistry20
- apastore
- Peter Cock
- Stephen Turner21
- 1. Ginkgo Bioworks
- 2. Harvard Chan School of Public Health
- 3. @CenterForMedicalGeneticsGhent
- 4. @hsph-qbrc
- 5. University of Melbourne
- 6. Lund University Cancer Center
- 7. @populationgenomics
- 8. @iZettle
- 9. Science for Life Laboratory
- 10. AstraZeneca
- 11. startup
- 12. The University of Melbourne
- 13. Recurse Center
- 14. University of Rostock
- 15. Aalborg University
- 16. @tss-yonder
- 17. Serqet Therapeutics
- 18. University of Utrecht
- 19. @related-sciences
- 20. HSPH
- 21. @signaturescience
Description
- Set ENCODE library complexity flags properly for ChIP-seq. Thanks to @mistrm82.
- Fix greylisted peaks not being propagated to the output directory. Thanks to @mistrm82.
- Better error message when no sample barcodes are found for single-cell RNA-seq.
- Better trimming for 2 wgbs kits
- enable setting parameters for deduplicate_bismark
- custom threading for bismark via yaml
- reproducible WGBS user story with the data from Encode
- While consensus peak calling, keep the highest scoring peak instead of calling the summit for the highest scoring peak and expanding the peak to 250 bases.
- Enable consensus peak calling for broad peaks. Thanks to @mistrm82 and @yoonsquared for pointing out this was missing.
- Re-enable ATAC-seq tests, they work now.
- svprioritize for mm10
- purecn_Dx.R - mutational signatures - still requires a manual update of deconstructsigs or release of it
- make sure purecn uses sv_regions bed to call variants
- fix misleading disambiguation fastqc read statistics (total, hg38, mm10)
- wgbs: nebemseq kit: add --maxins 1000 and --local to bismark align
- WGBS: sorted indexed deduplicated bam for ready.bam
- print error message when aligner: false and hla typing is on
- make sure that mark_duplicates is false with collapsed UMI input
Files
bcbio/bcbio-nextgen-v.1.2.8.zip
Files
(17.8 MB)
| Name | Size | Download all |
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md5:73866eb0586a7fd8553899a0486b4a8d
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Additional details
Related works
- Is supplement to
- https://github.com/bcbio/bcbio-nextgen/tree/v.1.2.8 (URL)