krakenUniq+Bracken

[YiJessePi]

Hello, We are currently using kraken2+bracken but would definitely want to use the advantages of krakenuniq to identify unique kmers to reduce false classification. I came across this publication who states:

"If counting all listed taxa, regardless of low readcounts, the Kraken2 is known to produce many false positives [32], i.e., list taxa as present when they are in fact not. The KrakenUniq software has been developed to handle this problem [32]. We ran it to classify the metagenome reads for both healthy and IBD metagenomes. The overall results from both Kraken2 and KrakenUniq tools were similar, but KrakenUniq also reports the number of unique k-mers in each genome covered by the reads. On the other hand, only Kraken2 reports are compatible for running the Bracken software. Since we were interested in both—that is finding the true positive identifications, and their estimated abundances—we combined the two approaches."

Is krakenuniq indeed not compatible with bracken? What do you think about this suggested flow? kraken2->filtering by krakenuniq->bracken?

[jenniferlu717]

Bracken should work with KrakenUniq output (but there may be some formatting issues that I have yet to fix - if you find this, please submit another request).

Kraken2 does now incorporate the KrakenUniq unique kmer counts, if you specify another parameter. (see the Kraken2 github for this)

[nick-youngblut]

Bracken should work with KrakenUniq output (but there may be some formatting issues that I have yet to fix - if you find this, please submit another request).

Any progress on this?