pyScaf
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lpryszcz
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Hi, I would just like to make a return on the scaffolding of my assembly (Sanger technology) with PacBio reads (30x coverage), by using pyScaf. pyScaf is fast and generates...
Hi, I'm currently scaffolding an assembly with some Nanopore data, but it is somewhat difficult to figure out the status of this job. There is no output to a logfile...
Hi, The program seems running, but stuck at the beginning of **aligning contigs on reference**, 12 hours no progress... Any suggestion? Thanks.
Hi, I ran the following command: pyScaf -f assembly.fa -o pyscaf.scaffolding -t 64 --log pyscaf.log --dotplot png -n pacbio_reads.fasta It blocks and I receive the output as in the image....
Hello : I had use conda install fastaindex; but I still got the eroor My command is : `./pyScaf.py -f assembly.fasta -n long-read.fasta -o mapped@pyS` Is there any problems with...
Hi, I do not know if it is a silly error... but I am trying to run pyScaf to do scaffolding in my Canu (Pabio) assembly with my nanopore reads....
Hi, I'm trying to run the example commands and getting the following error: ``` ./pyScaf.py -f test/contigs.reduced.fa -r test/ref.fa -o test/contigs.reduced.ref.fa Options: Namespace(dotplot='png', fasta='test/contigs.reduced.fa', fastq=None, identity=0.33, joins=5, linkratio=0.7, load=0.2, log=,...
The script terminated with an error message: ... return self._populate_scaffold(links, end, sid, scaffold, orientations, gaps, orientation) File "./pyScaf.py", line 307, in _populate_scaffold return self._populate_scaffold(links, end, sid, scaffold, orientations, gaps, orientation)...
I have get as long as ~500K bp gaps when using PacBio reads for scaffolding. However, the long reads are not longer than 80K. I wonder how such long gaps...
as in topic [mail](https://mail.google.com/mail/u/0/#sent/15b4ea60cfbd28cb)
