User: Rayan Chikhi

gravatar for Rayan Chikhi
Rayan Chikhi1.1k
Reputation:
1,140
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Trusted
Location:
France, Lille, CNRS
Website:
http://twitter.com/Ray...
Last seen:
3 days, 12 hours ago
Joined:
4 years, 7 months ago
Email:
r******@gmail.com

Posts by Rayan Chikhi

<prev • 202 results • page 1 of 21 • next >
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Comment: C: What's a good PacBio CLR read simulator?
... this worked well for me, and easy to install, thanks. ...
written 4 weeks ago by Rayan Chikhi1.1k
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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 7 weeks ago by Rayan Chikhi1.1k
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Answer: A: Kmergenie fails to fit models with --diploid settings
... 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 7 weeks ago by Rayan Chikhi1.1k
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Answer: A: Kmergenie k-mer estimate and multiple k-mers
... 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 7 weeks ago by Rayan Chikhi1.1k
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Comment: C: compiling kmergenie 1.7038. Is it possible?
... 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 7 weeks ago by Rayan Chikhi1.1k
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Answer: A: compiling kmergenie 1.7038. Is it possible?
... 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 7 weeks ago by Rayan Chikhi1.1k
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Answer: A: kmergenie Installation failed. seems got a bug
... 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 7 weeks ago by Rayan Chikhi1.1k
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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 7 weeks ago by Rayan Chikhi1.1k
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Answer: A: GATB Multithread always one core
... 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 7 weeks ago by Rayan Chikhi1.1k
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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 7 weeks ago by Rayan Chikhi1.1k

Latest awards to Rayan Chikhi

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Scholar 11 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 14 months ago, received more than 100 upvotes.
Popular Question 19 months ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question 20 months ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated 22 months ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 2.2 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 2.2 years ago, created 100 posts.
Appreciated 2.6 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Scholar 2.7 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Voter 2.7 years ago, voted more than 100 times.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Appreciated 2.9 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Supporter 3.0 years ago, voted at least 25 times.
Student 3.1 years ago, asked a question with at least 3 up-votes. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Tool Recommendations For Human Genome Assembly
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure

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