User: Rayan Chikhi
Rayan Chikhi • 1.3k
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- France, Lille, CNRS
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Posts by Rayan Chikhi
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... Have a look at https://github.com/rrwick/Unicycler ...
written 1 day ago by
Rayan Chikhi • 1.3k
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... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 12 days ago by
Rayan Chikhi • 1.3k
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... 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 Chikhi • 1.3k
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... Are you running it on a network drive? also, how many threads and free disk space? ...
written 8 weeks ago by
Rayan Chikhi • 1.3k
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... 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 Chikhi • 1.3k
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... 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 Chikhi • 1.3k
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... 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 Chikhi • 1.3k
• updated
5 months ago by
Ram ♦ 14k
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... 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 Chikhi • 1.3k
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... 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 Chikhi • 1.3k
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... 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 Chikhi • 1.3k
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For C: confusion in the DeBruijn Graph
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For A: How to determine appropriate value for abundance parameter?
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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For Fast kmer reverse complement code using bit tricks
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For C: Kmergenie histogram file
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For A: How to determine appropriate value for abundance parameter?
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For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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For A: Illumina Assembly Gap Closure
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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