User: Rayan Chikhi
Rayan Chikhi • 1.4k
- Reputation:
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- Location:
- France, Lille, CNRS
- Website:
- http://twitter.com/Ray...
- Last seen:
- 6 hours ago
- Joined:
- 5 years, 11 months ago
- Email:
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Posts by Rayan Chikhi
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... 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 10 days ago by
Rayan Chikhi • 1.4k
1
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1
answer
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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 18 days ago by
Rayan Chikhi • 1.4k
2
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1
answer
142
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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 7 weeks ago by
Rayan Chikhi • 1.4k
1
vote
1
answer
712
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... 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 12 weeks ago by
Rayan Chikhi • 1.4k
0
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1
answer
277
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1
answers
... Have a look at https://github.com/rrwick/Unicycler ...
written 3 months ago by
Rayan Chikhi • 1.4k
4
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1
answer
712
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... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 4 months ago by
Rayan Chikhi • 1.4k
0
votes
1
answer
302
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1
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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 5 months ago by
Rayan Chikhi • 1.4k
0
votes
1
answer
302
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1
answers
... Are you running it on a network drive? also, how many threads and free disk space? ...
written 6 months ago by
Rayan Chikhi • 1.4k
3
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1
answer
302
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1
answers
... 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 6 months ago by
Rayan Chikhi • 1.4k
0
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2
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405
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2
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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 9 months ago by
Rayan Chikhi • 1.4k
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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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2.2 years ago,
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For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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