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sn_detectContamination.pl.md

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SYNOPSIS

sn_detectContamination.pl

Runs a kmer histogram to detect potential contamination.

Software requirements

  • Perl module Bio::Kmer

Algorithm

Runs a kmer histogram. The null hypothesis is that there will be a peak around 1x coverage due to errors in sequencing, and a second peak around the expected genome coverage. If something else were sequenced at the same time at a different coverage, then there will be another peak at that coverage level. This other peak will be indicative of potential contamination.

Outputs

Table with columns

  • File
  • numPeaks
  • finalDelta - the amplitude difference between one coverage and the next to determine what a valley is
  • hist - ascii representation
  • firstPeak - coverage for the first peak
  • firstValley - coverage for the first valley
  • secondPeak
  • secondValley...

More columns are possible with additional valleys