Humann3 / Missing pick-frames option

Microbial community profiling HUMAnN
1

Dear Humann3 team,

I am a user of your software and have been using the pick-frames option for the alignment of protein sequences. However, I noticed that this option is no longer available in the latest version of Humann3. I am wondering if this option has been removed or if it has been incorporated into another feature.

Could you please provide some information on the status of the pick-frames option in Humann3? If it has been removed, what alternatives are available for the alignment of protein sequences?

Thank you for your time and assistance.

Best regards,
Jérémy Tournayre

2

--pick-frames was largely a relic from when we were using RAPSearch2 in the early HUMAnN 2 prototype, where picking among the six possibly translation frames for each read upstream of search gave a speedup. DIAMOND, which we now use for translated search, does a version of this picking internally, so using --pick-frames just added to the runtime without any real benefit. We eventually deprecated the feature to help simplify the CLI.

1 Like