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khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics
http://www.recentrifuge.org
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Rextract from Kraken2 output #46

Closed buiguesj closed 11 months ago

buiguesj commented 2 years ago

Question

I tried to run rextract with a kraken2 output but I get the following warning message: No matching read found! Exiting. Is there a way to extract reads from kraken2 output or it's just made to run with Centrifuge output files??

khyox commented 2 years ago

Hi @buiguesj — Rextract is oriented to Centrifuge's output. However, it had some support for Kraken output. To test if it supports your version, just try the same command you used but with with -i 1 (root) instead of -i 10239. If you get some output, then you have support and you just entered a sample without viruses, if you don't, then you haven't support.