verkkofillet.tl.calQV

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verkkofillet.tl.calQV#

verkkofillet.tl.calQV(obj, working_directory='kmer', prefix='assembly', fasta='assembly.fasta', k=31, showOnly=False, trio=False, contig_prefix=['dam', 'sire'])[source]#

Perform quality evaluation using Merqury’s qv.sh script.

Parameters:

  • obj – Object containing the verkkoDir attribute.

  • working_directory – The working directory for the analysis. Default is “kmer”.

  • prefix – Prefix for the meryl output. Default is “assembly”.

  • fasta – Path to the assembly FASTA file. Default is “assembly.fasta”.

  • k – The k-mer size. Default is 31.

  • showOnly – If True, only show the command line without running it. Default is False.

  • trio – If True, the assembly is going to split into maternal and paternal haplotypes. Default is False.

  • contig_prefix – Prefixes for the maternal and paternal haplotypes. Default is [“dam”, “sire”]. This is only used if trio is True. If trio mode is off, this parameter is ignored.

Returns:

{prefix}.qv_cal.qv

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