User: Rayan Chikhi
Rayan Chikhi • 1.2k
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Posts by Rayan Chikhi
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... Apologies, I do not get Biostar notifications through my email for some reasons. How much disk space and memory do you have on this machine? Did you end up getting an assembly with version 2.0.7? If not, I could advise trying the very latest version from the Github, following the compilation instruc ...
written 23 days ago by
Rayan Chikhi • 1.2k
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... This was resolved through an email discussion. A possible fix is to use the "-max-memory 5000", but I believe that the problem is being fixed in by using more recent version of Minia (https://github.com/GATB/minia). ...
written 23 days ago by
Rayan Chikhi • 1.2k
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... Hi, yes Minia should keep singleton k-mers that were not filtered out by the abundance threshold. You can check this by looking at the length of the smallest contigs.
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written 23 days ago by
Rayan Chikhi • 1.2k
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... this worked well for me, and easy to install, thanks. ...
written 6 months ago by
Rayan Chikhi • 1.2k
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Comment:
C: One Sided Contig Extension
... might not perform exactly how you want, but you could give [Mapsembler2][1] or [Kollector][2] a try
[1]: https://colibread.inria.fr/software/mapsembler2/
[2]: https://github.com/bcgsc/kollector ...
written 6 months ago by
Rayan Chikhi • 1.2k
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... for the record: Pepijn and I communicated by email, and the diploid model has been improved in recent kmergenie versions, hopefully addressing this issue. ...
written 6 months ago by
Rayan Chikhi • 1.2k
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... Hi,
Apologies for the delay to answer, I'm not getting Biostar notifications lately.
(a): if you're doing multi-k assembly, I'd recommend using the default k values from the assembler unless you have a good reason not to. Adding a more k values in-between the min-k and the max-k should not hurt th ...
written 6 months ago by
Rayan Chikhi • 1.2k
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... Hi Brian,
The theoretical foundations of kmergenie can be found in Section 2 of [our article][1]. Please feel free to email us if any detail was unclear there.. This article was published in 2013 but I continue to believe that the theoretical grounds there still hold for past and current Illumina s ...
written 6 months ago by
Rayan Chikhi • 1.2k
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... Hi, kmergenie has been updated to version 1.7039, hopefully it resolves this compilation issue. Please let me know if it doesn't. (kmergenie@cse.psu.edu) ...
written 6 months ago by
Rayan Chikhi • 1.2k
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... hi, I've updated kmergenie to version 1.7039, hopefully resolving this compilation issue. Please let me know if it still persists.
Thanks for the help Hamid. Any chance ntCard could get rid of automake/autoconf by the way? ...
written 6 months ago by
Rayan Chikhi • 1.2k
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