User: Rayan Chikhi
Rayan Chikhi • 1.2k
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- France, Lille, CNRS
- Website:
- http://twitter.com/Ray...
- Last seen:
- 3 weeks, 5 days ago
- Joined:
- 4 years, 10 months ago
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- r******@gmail.com
Posts by Rayan Chikhi
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... this worked well for me, and easy to install, thanks. ...
written 3 months ago by
Rayan Chikhi • 1.2k
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181
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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 4 months ago by
Rayan Chikhi • 1.2k
0
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1
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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 4 months ago by
Rayan Chikhi • 1.2k
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527
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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 4 months ago by
Rayan Chikhi • 1.2k
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419
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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 4 months ago by
Rayan Chikhi • 1.2k
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419
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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 4 months ago by
Rayan Chikhi • 1.2k
0
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2
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225
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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 4 months ago by
Rayan Chikhi • 1.2k
0
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264
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0
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Comment:
C: No best K value found
... hi, can you please post the first 4 lines of your fastq file? ...
written 4 months ago by
Rayan Chikhi • 1.2k
0
votes
1
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227
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... Hi,
We've found the issue here, thank to @grizk. Please change
IDispatcher::Status status = dispatcher.iterate (it, Functor());
to
IDispatcher::Status status = dispatcher.iterate (it, Functor(), 1);
This is because the third argument of iterate() is a batch size, i.e. a number of itera ...
written 4 months ago by
Rayan Chikhi • 1.2k
0
votes
1
answer
227
views
1
answers
Comment:
C: GATB Multithread always one core
... indeed, I can confirm the issue. For some reason the dispatcher only uses one core in that setting. Will see how to suggest fix. ...
written 4 months ago by
Rayan Chikhi • 1.2k
Latest awards to Rayan Chikhi
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6 weeks ago,
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For Fast kmer reverse complement code using bit tricks
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For C: Kmergenie histogram file
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For A: How to determine appropriate value for abundance parameter?
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13 months ago,
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For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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17 months ago,
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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23 months ago,
created a question with more than 1,000 views.
For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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For A: How to determine appropriate value for abundance parameter?
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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