User: Rayan Chikhi

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

<prev • 215 results • page 1 of 22 • next >
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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 1 day 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 12 days 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 8 weeks 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 8 weeks 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 9 weeks 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 5 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 5 months ago by Rayan Chikhi1.3k • updated 5 months ago by Ram14k
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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 5 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 5 months ago by Rayan Chikhi1.3k
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Answer: A: compiling gatb-core with external Boost and hdf5
... Hi Ilya, the short answer is that you currently cannot as of today. A GATB team member attempted to do that before, but this entails to modify gatb's CMakeLists.txt to find the system boost and hdf5 libs, as well as a few #include's. Currently the easiest solution is to ship (a subset of) boost an ...
written 6 months ago by Rayan Chikhi1.3k

Latest awards to Rayan Chikhi

Commentator 10 days ago, created a comment with at least 3 up-votes. For C: confusion in the DeBruijn Graph
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar 5 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question 10 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Popular Question 15 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Good Answer 22 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 23 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 2.2 years ago, received more than 100 upvotes.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated 2.9 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Scholar 3.1 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 3.2 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 3.2 years ago, created 100 posts.
Appreciated 3.6 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
Scholar 3.7 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Voter 3.7 years ago, voted more than 100 times.
Popular Question 3.7 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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