Adding read filters - Githubissues

fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

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Open fbreitwieser opened 6 years ago

fbreitwieser commented 6 years ago

Re #7 : Consider adding read-level scores and thresholds. Possible scores:

kraken-filter score: taxon_kmers / unambiguous_kmers
Andersen score: `taxon_kmers / unambiguous_kmers * (1 - unassigned_kmers / unambiguous_kmers)

Read get promoted to higher taxa until a threshold is met.

yi1873 commented 6 years ago

Is the score between 0 and 1 calculated as taxon_kmers / unambiguous_kmers * (1 - unassigned_kmers / unambiguous_kmers) ?

fbreitwieser commented 6 years ago

Yep. unambiguous_kmers is all k-mers without an N.

unambiguous_kmers = unassigned_kmers + taxon_kmers + kmers + assigned_to_other_taxa