new release any time soon?

[derrickwood]

new release any time soon?

[lynxoid]

Maybe Braken (http://biorxiv.org/content/early/2016/05/05/051813) is delaying the update process?

[cjfields]

May be some issues with the recent NCBI changes from GI to Accession.Version, see issue #50

[taltman]

Thanks for pointing out Bracken, @lynxoid!

[Andreas-Bio]

Is kraken still okay? Will it be improved? Does it have support? I am starting a 3 year project and I do not want to start using something that is slowly falling apart, as you can see with the GenBank ID issue.
Are there alternatives?
I "only" have 300.000 reads with a length of 900, but naive Bayes is still too slow for me (and random forest ans SVM).

[Redmar-van-den-Berg]

I think kraken will be ok, the original maintainer has moved on but there is still interest in the program, and I've been working on adding support for Accession instead of GI. You can see some discussions about that here (#68). I think the best course of action is to ask the developer of Bracken if they want to take over support, since their work requires Kraken as well. https://github.com/jenniferlu717/Bracken

[jenniferlu717]

Hi, As the developer of Bracken, I was not intending on taking over support of Kraken but our lab in general is working through some upgrades/updates to Kraken. @DerrickWood also has an updated version that should address the GI numbers (from what I have heard). I'm not sure when we will release the updates but hopefully it will be soon.

As we still use Kraken within our lab for our projects, we have not abandoned the software but have delayed working on it as Derrick Wood is still the primary owner/developer of the Kraken software.

[jenniferlu717]

Derrick just made a fix to the phasing out of NCBI GI numbers so the new version should work properly. If not, please create a new issue and let us know. Thanks,