Report #

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

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

Example report

[[step]]
    action = 'Report'
    name = "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 segment. Full match only, no iupac
    count_oligos_segment = "all" # segment to count oligos in, can be 'all', 'read1', ...
    tag_histograms = ["mytag"] # Calculate a histogram for this tag

Statistics available (for each ‘segment’. If demultiplexed, 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)

Histograms #

When histograms are enabled, a {value: count} object is embedded into the json report, and visualized as a bar chart in the html reports.

Keys (values) are always strings in the report due to a json limitation. Numeric values are rounded to the next integer. Boolean values are represented as ’true’ and ‘false’. Location & String tags are quantified by their (replaced) string contents.

Note that the html histograms only show the first 100 entries, full data is always in the json.