User: Rayan Chikhi
Rayan Chikhi • 1.3k
- Reputation:
- 1,310
- Status:
- Trusted
- Location:
- France, Lille, CNRS
- Website:
- http://twitter.com/Ray...
- Last seen:
- 7 hours ago
- Joined:
- 5 years, 9 months ago
- Email:
- r******@gmail.com
Posts by Rayan Chikhi
<prev
• 216 results •
page 1 of 22 •
next >
1
vote
1
answer
550
views
1
answers
... 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 22 days ago by
Rayan Chikhi • 1.3k
0
votes
1
answer
146
views
1
answers
... Have a look at https://github.com/rrwick/Unicycler ...
written 8 weeks ago by
Rayan Chikhi • 1.3k
4
votes
1
answer
550
views
1
answers
... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 9 weeks ago by
Rayan Chikhi • 1.3k
0
votes
1
answer
253
views
1
answers
... Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds? ...
written 3 months ago by
Rayan Chikhi • 1.3k
0
votes
1
answer
253
views
1
answers
... Are you running it on a network drive? also, how many threads and free disk space? ...
written 3 months ago by
Rayan Chikhi • 1.3k
3
votes
1
answer
253
views
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 4 months ago by
Rayan Chikhi • 1.3k
0
votes
2
answers
350
views
2
answers
... 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 6 months ago by
Rayan Chikhi • 1.3k
0
votes
1
answer
375
views
1
answers
... 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 7 months ago by
Rayan Chikhi • 1.3k
• updated
7 months ago by
Ram ♦ 15k
0
votes
1
answer
408
views
1
answers
... 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 7 months ago by
Rayan Chikhi • 1.3k
2
votes
1
answer
347
views
1
answers
... 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 7 months ago by
Rayan Chikhi • 1.3k
Latest awards to Rayan Chikhi
Commentator
9 weeks ago,
created a comment with at least 3 up-votes.
For C: confusion in the DeBruijn Graph
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How to determine appropriate value for abundance parameter?
Scholar
4 months ago,
created an answer that has been accepted.
For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar
7 months ago,
created an answer that has been accepted.
For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Fast kmer reverse complement code using bit tricks
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: Kmergenie histogram file
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: How to determine appropriate value for abundance parameter?
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Fast kmer reverse complement code using bit tricks
Good Answer
2.0 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
2.1 years ago,
created an answer that has been accepted.
For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru
2.3 years ago,
received more than 100 upvotes.
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated
3.0 years ago,
created a post with more than 5 votes.
For GATB will provide developer support via Biostar
Teacher
3.1 years ago,
created an answer with at least 3 up-votes.
For A: How to determine appropriate value for abundance parameter?
Teacher
3.2 years ago,
created an answer with at least 3 up-votes.
For A: Illumina Assembly Gap Closure
Scholar
3.2 years ago,
created an answer that has been accepted.
For A: Choosing K-mer size in Kmergenie for denovo assembly
Commentator
3.2 years ago,
created a comment with at least 3 up-votes.
For C: Kmergenie histogram file
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For Fast kmer reverse complement code using bit tricks
Centurion
3.4 years ago,
created 100 posts.
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For GATB will provide user support via Biostar
Scholar
3.8 years ago,
created an answer that has been accepted.
For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher
3.8 years ago,
created an answer with at least 3 up-votes.
For A: Illumina Assembly Gap Closure
Voter
3.9 years ago,
voted more than 100 times.
Popular Question
3.9 years ago,
created a question with more than 1,000 views.
For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 933 users visited in the last hour