User: Rayan Chikhi

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Rayan Chikhi1.3k
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France, Lille, CNRS
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Posts by Rayan Chikhi

<prev • 216 results • page 1 of 22 • next >
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Comment: C: Want to use fastq-dump to download pacbio data? Read this before
... I think Bastien wants to know why we think the output of fastq-dump is "wrong". I recall it has to do with how the raw .bax.h5 PacBio files get converted to FASTQ. There seems to be additional step(s) needed in order to split raw reads and avoid chimeric reads. `dextractor` does them, but `fastq-dum ...
written 22 days ago by Rayan Chikhi1.3k
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Answer: A: Hybrid assembly using MinION data + correction with Illumina. Which strategy to
... Have a look at https://github.com/rrwick/Unicycler ...
written 8 weeks ago by Rayan Chikhi1.3k
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Comment: C: Want to use fastq-dump to download pacbio data? Read this before
... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 9 weeks ago by Rayan Chikhi1.3k
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Comment: C: Minia assembler restart after error?
... Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds? ...
written 3 months ago by Rayan Chikhi1.3k
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Comment: C: Minia assembler restart after error?
... Are you running it on a network drive? also, how many threads and free disk space? ...
written 3 months ago by Rayan Chikhi1.3k
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Answer: A: Minia assembler restart after error?
... Hi, due to the use of HDF5, the intermediate files do not get properly saved during a run, hence it's generally not possible to restart a minia run. What sort of organism took 72+ hours to assemble? This might be a good occasion to use the latest version of minia (https://github.com/GATB/minia, comp ...
written 4 months ago by Rayan Chikhi1.3k
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Answer: A: Is there any plant-specific genome assembler?
... I'll mention this one, that is a fork of Discovar that was used to assemble a wheat: https://github.com/bioinfologics/w2rap-contigger ...
written 6 months ago by Rayan Chikhi1.3k
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Answer: A: GATB-minia-pipelne fails at bloocoo step
... Glad you were able to solve it. Note also that it is possible to run gatb-minia-pipeline without bloocoo, using the `--no-error-correction` flag. If you have any other issues, please let us know. ...
written 7 months ago by Rayan Chikhi1.3k • updated 7 months ago by Ram15k
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Answer: A: importing a GFA2 scaffold graph
... Hi! I hope the answer is still relevant now. Converting GFA2 to HDF5 doesn't make much sense in GATB: the info that we store inside the HDF5 actually consists of k-mers counts and a Bloom filter (and other stuff). So the graph stored in a .h5 is a regular de Bruijn graphn and cannot be of any othe ...
written 7 months ago by Rayan Chikhi1.3k
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Answer: A: GATB - Multithreaded iteration of paired banks ?
... There was a tricky long-standing bug in GATB where PairedIterator did not work in conjunction with Dispatcher. I just fixed it, if you update to the master branch of gatb-core, it should work. You can also try the new tools/multithreading8.cpp example that illustrates PairedIterator with Dispatcher ...
written 7 months ago by Rayan Chikhi1.3k

Latest awards to Rayan Chikhi

Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: confusion in the DeBruijn Graph
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 4 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar 7 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question 12 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Popular Question 16 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Good Answer 2.0 years 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 2.1 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 2.3 years ago, received more than 100 upvotes.
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
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
Appreciated 3.0 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Scholar 3.2 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 3.4 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 3.4 years ago, created 100 posts.
Appreciated 3.7 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Scholar 3.8 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Voter 3.9 years ago, voted more than 100 times.
Popular Question 3.9 years 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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