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Hello,
I meet a question when using the software . my command line likes this :
python2 ./run_pipeline.py -a ONTmin.fasta -l ONTmin.fasta.fai -b ONT.sort.REduced.paired_only.bed -e {AAGCTT} -o scaff…
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I'm interested in your tool after watching the report of Bjorn Usadel at 2017 London Calling.
I'm assembling an animal genome which is repeat-rich. I haven't got good assembly yet and want to test yo…
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```
gfak fillseq -f nonexistant.fa canu.unitigs.gfa >/dev/null; echo $?
Error: couldn't open fasta file nonexistant.fa
0
```
Expected behaviour: the exit status should be non-zero (`1`).
```
…
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Hello,
In the process of assembling contig, I did not produce the file of contigs_graph.gfa and unitigs_graph.gfa, only the data of contig and HIC. How should I assemble the scaffold with SALSA?
bes…
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Hi -
I am trying to tun salsa on a CANU assembly. I tried a first time with contigs and assembly graph (.gfa).
However, the pipeline stops during iteration 2 at this step:
`make_links.py -b tes…
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Hello all,
I am at Schloss Dagstuhl with Gene Myers, Jason Chin, Adam Phillipy and others. We would like to propose a major revision to GFA that addresses a number of issues raised in particular by …
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The -u option specifies "The tiling of unitigs to contigs in bed format"
But its use should be made more explicit.
First, the guide should describe how this bed file is structured, as the bed forma…
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In the GRAPHS section of the [tutorial](https://github.com/marbl/canu/blob/master/documentation/source/tutorial.rst#outputs) the caveat on \.contigs.gfa regarding bubble edges is unclear. Nowhere is t…
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I have 2 flowcells of nanopore data for a Drosophila species and I have been repeatedly assembling decent sized, but erroneous contigs that map to multiple chromosomes. To try to get to the bottom of …