Version 1.3.0

Source code (zip) and Source code (tar.gz) are generated by GitHub and may not contain all required submodules. Use these at your own risk! It is suggested to use the release-source.zip if downloading the source code.

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

Date Created:

• 27 October 2023

General changes:

• Clean up Makefile

New subcommand:

• bc: Extracts cell barcode from reads. Useful for single-cell experiments that utilize cell barcodes.
  • For usage, run biscuit bc -h

Changes affecting specific subcommands/scripts:

• align:
  • FASTA/FASTQ read comments are now appended to read name when retained (biscuit align -C)
  • Add -9 option for extracting barcodes from read comment and placing in CR SAM tag.
• vcf2bed:
  • Add -c option to create Bismark .cov-like format (i.e., Beta-M-U columns)
• mergecg:
  • Add -c option to create Bismark .cov-like format (i.e., Beta-M-U columns)

Bug Fixes:

• Issue #38 fixed (unhelpful error message when FASTQ cannot be found). Reported by KChadwick78.
• Issue #41 fixed (SAM header not output to stdout). Reported by njspix.
• cinread workaround for long reads. Now only looks at the first 300 bases.
• Fix divide by zero error in QC.sh.
• Fix issue in mergecg when CG is at the end of the chromosome.
• Resolve segfault when passing empty SNP BED file to epiread.
• Fix sign error when calculating insert size distribution bounds.
• Fix incorrect formatting of bsstrand table output.