HumanN 4 release date

Microbial community profiling HUMAnN
1

Hello–I am just wondering when HumanN v4 is anticipated to be released? As I wanted to take advantage of MetaPhlan 4 in the functional analysis.

Thanks,

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2

Is there a rough idea of when it might be available yet? About to start a new project and wondering if it’s worth waiting for a new release or if I should proceed with HUMAnN 3. Thanks!

3

Hopefully by the end of this summer.

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4

Hello,
I am wondering if there will be an update of the uniref database used in the v4. It appears that certains uniref90 IDs from the v2019 are no more present in the actual uniref db.

5

Yes, we are planning a UniRef update for the alpha version of HUMAnN 4 and then a further update for the non-alpha release. Note that just because a protein is no longer a UniRef centroid it might still be in the database. You can try looking it up with the UniRef90_ prefix removed.

6

Hi, ok good news !
But no for certain uniprot ID they are no more in circulation. For instance: UniRef90_A0A0P6A1X1
A0A0P6A1X1 → search on uniprot gives only that:

This entry is obsolete since release 2019_10/2019_10

This entry has now been deleted. The protein sequence for this entry is available in UniParc.

7

Confirmed. Note that UniRef includes parts of UniParc (the UniProt Archive) in its clustering process, so it’s possible that a sequence in UniRef was already in UniParc when that version of UniRef was constructed (in which case you’d have to look to the UniParc entry for details about the protein). That said, based on the dates here it looks like the entry was obsoleted after our version of UniRef was built.

8

Wanted to start by saying I’m super grateful for all the hard work on this really useful tool. I was wondering if there were any updates on the expected release date for HumanN 4. Thanks!

9

The alpha release should be out very soon. I finished making a new demo for HUMAnN 4 last week, which was one of the last remaining tasks.

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10

Hi @franzosa , I wanted to check whether this is coming in the next month or two. We have Metaphlan4 runs and planned on using the HUMAnN4 alpha for the annotation, but if you think it’s best we could fall back to the latest HUMAnN v3 release and using the mapping files.

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11

That is the hope. The software is ready, but we discovered some issues with fragmentary genes in the database during late-stage testing that we are now working to correct. We will make a pinned post here as soon as everything is ready.

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12

Thx @franzosa for the quick response, I’ll keep an eye out for it!

13

Hi @franzosa , Thanks for developing the wonderful tools. Just wondering if there is any update on this now?