User: Rayan Chikhi

gravatar for Rayan Chikhi
Rayan Chikhi1.2k
Reputation:
1,250
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Location:
France, Lille, CNRS
Website:
http://twitter.com/Ray...
Last seen:
1 day, 19 hours ago
Joined:
5 years, 5 months ago
Email:
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Posts by Rayan Chikhi

<prev • 211 results • page 1 of 22 • next >
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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 days ago by Rayan Chikhi1.2k
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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 12 weeks ago by Rayan Chikhi1.2k
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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 3 months ago by Rayan Chikhi1.2k • updated 3 months ago by Ram13k
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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 3 months ago by Rayan Chikhi1.2k
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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 3 months ago by Rayan Chikhi1.2k
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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 4 months ago by Rayan Chikhi1.2k
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Comment: C: Minia stuck - I don't know if my routine is still running
... Apologies, I do not get Biostar notifications through my email for some reasons. How much disk space and memory do you have on this machine? Did you end up getting an assembly with version 2.0.7? If not, I could advise trying the very latest version from the Github, following the compilation instruc ...
written 5 months ago by Rayan Chikhi1.2k
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Answer: A: Error: MPHF is not injective in Minia
... This was resolved through an email discussion. A possible fix is to use the "-max-memory 5000", but I believe that the problem is being fixed in by using more recent version of Minia (https://github.com/GATB/minia). ...
written 5 months ago by Rayan Chikhi1.2k
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Answer: A: Does Minia discard singletons?
... Hi, yes Minia should keep singleton k-mers that were not filtered out by the abundance threshold. You can check this by looking at the length of the smallest contigs. ...
written 5 months ago by Rayan Chikhi1.2k
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Comment: C: What's a good PacBio CLR read simulator?
... this worked well for me, and easy to install, thanks. ...
written 11 months ago by Rayan Chikhi1.2k

Latest awards to Rayan Chikhi

Scholar 4 days ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar 3 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question 8 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Popular Question 12 months ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Good Answer 20 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 21 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 2.0 years ago, received more than 100 upvotes.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated 2.7 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 3.0 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 3.0 years ago, created 100 posts.
Appreciated 3.4 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar
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
Voter 3.6 years ago, voted more than 100 times.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Teacher 3.6 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 3.8 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar

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