User: Rayan Chikhi

gravatar for Rayan Chikhi
Rayan Chikhi1.4k
Reputation:
1,360
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Trusted
Location:
France, Lille, CNRS
Website:
http://twitter.com/Ray...
Last seen:
3 days, 13 hours ago
Joined:
6 years, 1 month ago
Email:
r******@gmail.com

Posts by Rayan Chikhi

<prev • 219 results • page 1 of 22 • next >
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Answer: A: Segmentation fault when running Minia v3 with some kmer values
... Hi, Segfault is unlikely a memory error but rather a bug in the program or something else. Do you have enough disk space? Would it be possible to share the input data? Best, Rayan ...
written 9 weeks ago by Rayan Chikhi1.4k
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Comment: C: GATB buildNode giving errors
... Hi, sorry I didn't get notified by the responses in this thread. In the future, please reach me at rayan.chikhi@univ-lille.fr if this happens! 1) Are you using the Graph or GraphUnitigs class? (seems that it is GraphUnitigs) 2) If you're using GraphUnitigs, the function you're looking for is debug ...
written 11 weeks ago by Rayan Chikhi1.4k
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Answer: A: GATB buildNode giving errors
... Hi, could you try changing "Node left" to "auto left" to see if it gets rid of the error? Best, Rayan ...
written 3 months ago by Rayan Chikhi1.4k
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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 4 months ago by Rayan Chikhi1.4k
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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 5 months ago by Rayan Chikhi1.4k
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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 6 months ago by Rayan Chikhi1.4k
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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 7 months ago by Rayan Chikhi1.4k
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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 7 months ago by Rayan Chikhi1.4k
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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 8 months ago by Rayan Chikhi1.4k
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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 10 months ago by Rayan Chikhi1.4k

Latest awards to Rayan Chikhi

Scholar 11 weeks ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: confusion in the DeBruijn Graph
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 8 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar 11 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question 16 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Popular Question 21 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Good Answer 2.4 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 2.4 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 2.7 years ago, received more than 100 upvotes.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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
Appreciated 3.3 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Commentator 3.5 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 3.7 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 3.7 years ago, created 100 posts.
Appreciated 4.1 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Scholar 4.2 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Voter 4.2 years ago, voted more than 100 times.

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