User: Rayan Chikhi

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Rayan Chikhi1.1k
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France, Lille, CNRS
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http://twitter.com/Ray...
Last seen:
5 days, 18 hours ago
Joined:
4 years, 7 months ago
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Posts by Rayan Chikhi

<prev • 202 results • page 2 of 21 • next >
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Answer: A: Minia estimated genome size
... Minia versions >= 2 do not need the genome size estimation anymore ...
written 4 months ago by Rayan Chikhi1.1k
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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 4 months ago by Rayan Chikhi1.1k
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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 8 months ago by Rayan Chikhi1.1k
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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 10 months ago by Rayan Chikhi1.1k
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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 10 months ago by Rayan Chikhi1.1k
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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 10 months ago by Rayan Chikhi1.1k
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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 11 months ago by Rayan Chikhi1.1k
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Comment: C: Minia crashes during kmer counting
... Hi, thanks for those details. 24.9 GB seems more in line with what Minia 3 typically uses. What I think was going on, is: * Minia version 2 had the "Pool allocation failed" that will be fixed in version 3. I told you to try with a higher memory limit but that didn't seem to be a valid workaround. ...
written 11 months ago by Rayan Chikhi1.1k
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Answer: A: List all solid k-mers with DSK
... Bonjour Alexandre, To output the solid kmers in string representation, you can either use the dsk2ascii tool provided with DSK, or parse the hdf5 file using h5dump. See https://github.com/GATB/dsk#results-visualization To integrate DSK results in a C++ program, it is currently recommended to use t ...
written 11 months ago by Rayan Chikhi1.1k
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Comment: C: Minia crashes during kmer counting
... Hi, it is quite unusual to see such a large memory usage. I wonder what is special about your data.. Can you please tell me the number of files and total size of the read dataset files, and the number of distinct kmers reported by minia 3 (possibly the full log of the output stats at the end). ...
written 12 months ago by Rayan Chikhi1.1k

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
Teacher 3 months 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 20 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 2.0 years 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 2.8 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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