Version 1.0.0 Alpha

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Date Created:

• 20 May 2020

Changes affecting BISCUIT, in general, or multiple subcommands/scripts:

• This version is not backwards compatible with BISCUIT Version 0.3.16 and earlier.
• Contact person for BISCUIT updated.
• biscuit markdup removed from API
• Unnecessary files removed from code base
• All subcommands now have a help option (-h)
• General consistency applied for help output
• Small changes to wording of option descriptions (default values included if not obvious)
• Error messages added for missing command line arguments
• Flag/option characters changes for consistency across subcommands (see next section for specific changes)

Changes affecting specific subcommands/scripts:

• bsconv:
  • Flag change: -b → -p for printing output in TSV format
• mergecg:
  • Flag change: -n → -N for NOMe-seq mode
• tview:
  • Flag change: -f was not originally being read, now is included
• epiread:
  • Flag change: -q → -@ for number of threads to use
• pileup:
  • Flag change: -q → -@ for number of threads
  • Flag change: added in -s flag for step of window dispatching
• align:
  • Flag change: -t → -@ for number of threads to use
  • Flag change: -h → -g for max number of hits output in XA tag
  • Flag change: -h now used for help
• QC.sh:
  • Updated script to reflect changes made to flag/option characters

Version 0.3.16

• Overhauled QC.sh to speed up running time
  • Changes were made to CLI
  • Changes made selection criteria for insert size
  • Duplicate rates calculated as number of reads marked duplicates, not bases
  • Bug fixed related to output of bisulfite strandedness (_strand_table.txt file)
  • Selection criteria for read-averaged cytosine retention rate was modified to match more closely with the selection criteria used for the base-averaged cytosine retention rate
  • Some metrics have been removed to speed up running and to try to keep to relevant QC metrics

Note, on 22 October 2020, new QC assets were uploaded. (The old assets can be found in old_(ref)_biscuit_qc_assets.zip.) These assets were generated using the build_biscuit_QC_assets.pl script. The only change to the mm10 and hg38 assets was 2 decimal precision for all GC-content windows (i.e. 0.2 is now 0.20). The hg19 CpG asset file is the same as before, but the GC-content assets have differences in the location of some of the highest (or lowest) windows for the bottom 10% (or top 10%) asset file. This change will affect the sequencing depth statistics table and the cumulative coverage plots found in the MultiQC report, but should be a fairly minor effect for relatively uniform libraries aligned with hg19.

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.15

• Updates to CLI of QC.sh
• Cleaning up underlying code in QC.sh
• Preparation for deprecation of biscuit markdup
• Remove help messages for pacbio and ont2d functionality until tested
• Change to CLI for biscuit pileup somatic mode

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.14

• New QC.sh interface.
• Output check from QC.sh
• Suppresses warning of bedtools in QC.sh
• Fix to exception when there is no duplicate reads
• Fix to when there is no non-CG cytosine pileup counts

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.13

Pre-release for Version 0.3.14

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.12

• Some performance tweaks, two rounds of seeding
• biscuit bsconv allows filtering by fraction of retention
• biscuit bsconv reports a summary of retention
• Allow for soft-clipping by base quality in alignment, see -z option in biscuit align
• Allow for additional soft-clipping in alignment see -5 and -3 in biscuit align

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.11

• Fix rare case where seeding skipped mapping non-unique reads because of asymmetric filtering

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.10

• A read mapping fix avoids seed chaining interference from the two bisulfite strands. This marginally improves on mapping in C-free or G-free regions.

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.9

• Important update: default alignment strand in changed -b 0 is the default and mapping happens at both strands. -b 1 (mapping happens only at parent strand, faster) is not by default
• Added rectangle subcommand to produce epi-read format of the same chromosome start and end

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!

Version 0.3.8

• Fix to tview hard clipping
• Fix to seed merging
• mergecg takes -k to filter minimum depth
• pileup optionally filters by minimum alignment score

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use at your own risk!