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; Stephen Turner
- 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
(17.8 MB)
| Name | Size | |
|---|---|---|
|
bcbio/bcbio-nextgen-v.1.2.8.zip
md5:73866eb0586a7fd8553899a0486b4a8d |
17.8 MB | Download |
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| Data volume | 3.5 GB | 195.8 MB |
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- Publication date:
- April 14, 2021
- DOI:
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- Related identifiers:
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- License (for files):
- Other (Open)