Version 1.0.0

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Important Note: This version is not backwards compatible with BISCUIT Version 0.3.16 and earlier.

Date Created:

• 17 September 2021

General Changes:

• 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)
• Perl script to generate QC asset files from a reference FASTA file (build_biscuit_QC_assets.pl)
  • For help in running: perl build_biscuit_QC_assets.pl -h
• Bash script added to flip PBAT reads in silico which makes viewing PBAT data in IGV easier (flip_pbat_reads.sh)
  • For help in running: bash flip_pbat_ready.sh -h

New Subcommands:

• qc Generate QC files from input BAM (does not include coverage of base-averaged methylation, use QC.sh for full QC)
• version Prints BISCUIT version

Changes affecting specific subcommands/scripts:

• asm:
  • Include check to see if input is in the correct format
• bsconv:
  • Flag change: -b → -p for printing output in TSV format
  • Split into header and implementation files
  • CpY filter added (functionality is similar to CpH filter, but restricted to CpC and CpT)
• bsstrand:
  • Split into header and implementation files
• cinread:
  • Split into header and implementation files
• epiread:
  • Flag change: -q → -@ for number of threads to use
  • Filters added to bring pileup and epiread filters into alignment
    • Includes filters for alignment score (-a), minimum base quality (-b), minimum distance to 5' and 3' ends of read (-5 and -3), and double counting overlapping bases (double counting avoided by default, -d allows double counting)
    • Default values are the same for the filters in both subcommands
  • Updated default to the epiBED format (see the documentation site for more details on the epiBED format)
  • Can output the old epiread format using the -O option
    • Can optionally print all CpG/GpC/SNP locations using the -A option in conjunction with -O (note, the output when running with -A is not compatible with rectangle)
• mergecg:
  • Flag change: -n → -N for NOMe-seq mode
• tview:
  • Flag change: -f was not originally being read, now is included
• pileup:
  • Flag change: -q → -@ for number of threads
  • Flag change: added in -s flag for step of window dispatching
  • Flag change: -e flag separated into two flags - -5 and -3
    • -5 is the minimum distance from the 5' end of the read (default: 3)
    • -3 is the minimum distance from the 3' end of the read (default: 3)
• 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
  • Updated script to include the qc subcommand
  • Added the [-n,--no-cov-qc] option to skip generating the coverage QC files
    • Greatly decreases the runtime when running with this option (especially for large datasets)

Bug Fixes:

• Fixed incorrect rounding of methylation fractions (Issue #7)
• Fixed bug where the minimum distance to end of read filter in pileup and epiread filtered one less base from the 5' end than requested (i.e., INT-1 bases were filtered for -e INT or -5 INT)
• CX INFO header line in pileup now prints correct CX tags when running in NOMe-seq mode