User: Rayan Chikhi

gravatar for Rayan Chikhi
Rayan Chikhi1.2k
Reputation:
1,190
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Location:
France, Lille, CNRS
Website:
http://twitter.com/Ray...
Last seen:
2 weeks, 6 days ago
Joined:
5 years ago
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r******@gmail.com

Posts by Rayan Chikhi

<prev • 205 results • page 2 of 21 • next >
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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 6 months ago by Rayan Chikhi1.2k
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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 6 months ago by Rayan Chikhi1.2k
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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 6 months ago by Rayan Chikhi1.2k
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Answer: A: Minia estimated genome size
... Minia versions >= 2 do not need the genome size estimation anymore ...
written 9 months ago by Rayan Chikhi1.2k
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Comment: C: Minia estimated genome size
... Indeed, Minia versions >= 2 do not need this parameter anymore (http://minia.genouest.org/) ...
written 9 months ago by Rayan Chikhi1.2k
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Comment: C: Mina recompile for larger kmer error
... which version of minia? the updated manual for version 2 on the website (http://minia.genouest.org/files/minia.pdf) has a different build method: `mkdir build && cd build && cmake -Dk4=160 .. && make -j 4` ...
written 13 months ago by Rayan Chikhi1.2k
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Answer: A: Minia bug with "--debloom original"
... No fix yet, I don't think I've tested that latest minia 3 on large genomes with k > 128 yet :) Thanks for pointing it out! Will let you know when a fix is out. ...
written 14 months ago by Rayan Chikhi1.2k
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Answer: A: kmergenie to estimate genome size and then sequencing coverage
... Hi, the discussion looks correct to me: it seems that you have ~650x coverage. Kmergenie can be used to predict an assembly size. But if you have already performed an assembly, then it is better to use the actual assembly size that you obtained. Note that for larger genomes, neither kmergenie, nor ...
written 15 months ago by Rayan Chikhi1.2k
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Answer: A: Segmentation fault error while using GATB
... Hi, It seems that the segfault occurs at the end of graph construction. What command line did you use? Also, could you try updating to the latest GATB-core ? (released version 1.2.0) Or even, latest one here: https://github.com/GATB/gatb-core/ ...
written 15 months ago by Rayan Chikhi1.2k
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Comment: C: Minia crashes during kmer counting
... Hi Erwan, Austin, I've implemented "-debloom original" in Minia for k>128. The change is now effective if you compile the source from Github, and it will be included in the next release of Minia 3. Austin, sure, you can use those results in a conference. Thanks for checking with us. Regarding ...
written 16 months ago by Rayan Chikhi1.2k

Latest awards to Rayan Chikhi

Popular Question 3 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Popular Question 7 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Good Answer 15 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 16 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 19 months ago, received more than 100 upvotes.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated 2.3 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 2.6 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 2.6 years ago, created 100 posts.
Appreciated 3.0 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Scholar 3.1 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Voter 3.1 years ago, voted more than 100 times.
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Teacher 3.2 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 3.3 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Supporter 3.4 years ago, voted at least 25 times.
Student 3.5 years ago, asked a question with at least 3 up-votes. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs

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