Identify total number of reads after host-removal not just %

Joon-Klaps / viralgenie

Detect iSNV and construct whole viral genomes from metagenomic samples

https://joon-klaps.github.io/viralgenie/

MIT License

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Identify total number of reads after host-removal not just % #85

Closed Joon-Klaps closed 6 months ago

Joon-Klaps commented 9 months ago

Description of feature

Total input reads after preprocessing (final step host removal) just reports a percentage but not a number. This should be a number. Because mqc doesn't annotate the kraken output, use a try and search for the following Consider checking for

Sample  Bacteria    Eukaryota   Archaea Other   Unclassified
LVE00136    63238.0 88.0    16.0    25.0    7798362.0
...

Here Bacteria or Eukaryota can be present but just not Viruses . Then the final column can be extracted.

Joon-Klaps commented 6 months ago

No need as fastqc is ran after host deduplication