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genomic-medicine-sweden / jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
GNU General Public License v3.0
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Intraspecies contamination check #183

Open LordRust opened 9 months ago

LordRust commented 9 months ago

The current QC parameters combined with Kraken gives a good indication of inter-species contaimination, but the only indication we get on intra-species contamination is more or less a high value for missing loci in combination with low N50 and other QC parameters showing OK values. We can plot a filtered histogram view of the frequency on ambiguous positions which is a clean way to verify intra-species contamination even for closely related strains.

ryanjameskennedy commented 2 months ago

Feel free to copy the perl script here @LordRust