Report

Report #

Capture data for the final report (see [..](output section)).

You can add multiple reports, at any stage of your transformation chain to get e.g. before/after filtering reports.

[[step]]
    action = 'Report'
    label = "report" # Key that the report will be listed under. Must be distinct
    count = true # count reads at this position
    base_statistics = false # include base distribution at each read position, q20, q30, total, gc bases
    length_distribution = false # capture read length distribution
    duplicate_count_per_read = false # count duplicates using Cukoo filter on each read1/read2/index1/index2
    duplicate_count_per_fragment = false # count duplicates using Cukoo filter, on concatenated read1/read2/index1/index2
    count_oligos = [] # if set, count these oligos in the target. Full match only, no iupac
    count_oligos_target = "all" # target to count oligos in, can be 'all', 'read1', ...

Statistics available (for each ‘segment’. If demultiplexd, per barcode combination):

  • read counts
  • total base count
  • bases count q20 or better
  • bases count q30 or better
  • read length distribution
  • AGTCN counts at each position
  • expected error rate at each position
  • duplicate count (if each read occurs twice, duplicate count = read count / 2)