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sn_passfail.pl.md

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SYNOPSIS

sn_passfail.pl

Marks each sample as passing or failing

Software requirements

Algorithm

Reads upstream plugins for pass/fail criteria. Currently these criteria are only coverage and read quality, from the read metrics plugin. Additionally, this includes Kraken contamination results. Contamination is conservatively set at 25% although anything over a smaller percentage might be reported as a warning in sn_detectContamination-kraken.pl.

Outputs

Table with columns

  • sample
  • assembly - if all sub quality checks pass, then this passes. If all are unknown, then this is unknown. If any fail, then this fails.
    • number of Ns (threshold defined in taxonProperties.conf) or number of genes
    • longest contiguous contig - longest tract of genome between two Ns
  • coverage - pass or fail
  • quality - pass or fail
  • kraken - pass or fail

1 indicates failure; 0 indicates pass; -1 indicates unknown (e.g., if Kraken was never run)