Available CCseqBasic pipeline versions

updated by Jelena - 16:00 03/Dec/2018

Current releases - fixes and issues

Bug fixes and updates (after release)

Current issues - known bugs and development targets !

CB5 - CCseqBasic5 ("Currently developed CC5") Fully portable. Released 20Nov2017.

  • Current development version of CCseqBasic
  • Download in GitHub - (may or may not be stable)
  • CB5 is like CS5 below - but getting all new fancy features.

    • New features, which not yet in CS5 pipe :

  • Partial support to Tiled Capture-C
  • UMI support with --UMI flag : not fully functional yet.


    • CS5 - CCseqBasic5 ("Stable portable CC5") Fully portable. Released 17Nov2017.

  • Current stable version of CCseqBasic
  • Receives features once they become stable in CB5 pipe (above)
  • Otherwise CS5 is like CF5 below.
  • Download in GitHub - (current version)
  • Development endpoints available as GitHub RELEASES

    • New features (after first release) :

  • PIPE_fastqPaths.txt to support multilane runs
  • Support to .gz packed fastq files with --gz flag
  • Bowtie2 support --bowtie2 (please note that some issues with multimapping-related duplicate-filtering still remain)

    • New features (at the time of first release) :

  • Wobbly end duplicate filter with --wobblyEndBinWidth flag : non-exact-read-ends duplicate filtering.
    • To turn wobbly ends off, set this to 1 ( --wobblyEndBinWidth 1 ) - this is the default.
    If using --UMI , --wobblyEndBinWidth 20 is recommended.

    For example : --wobblyEndBinWidth 20 means : bin of 20 bases for duplicate filter :
    if all fragment coordinates are the same +/- 10 bases, ( and if --UMI is used : UMI is the same), reads are duplicates.

    CF5 - CCseqBasic5 ("Frozen portable CC5") Fully portable. Only receiving bug fixes.

  • First release of CCseqBasic as a single pipeline
  • Combines earlier development branches CB3 and CB4
  • Frozen in development to 16Nov2017

    • Introducing "third way to filter non-flashed reads" :
    Because: CF3 is too lenient to duplicates (of non-flashable reads) and CF4 is too strict - CF5 is "in between" (just goldilocks).

    In CF5 all the pipes merge to a single run command :
    User can call the wanted duplicate filtering mode with --CCversion CF3 or --CCversion CF4 or --CCversion CF5