Comments (5)
The point of Recycler and it's successor SCAPP is that they use the structure of the assembly graph which encodes much more information than the contigs or scaffolds. These tools will not work with just the contig or scaffold files as these do not include the graph structure.
If you can let us know more about what you're trying to do we can help you run SCAPP or Recycler on your data.
from recycler.
Thanks @dpellow. I have a single-end oxford nanopore reads of mycobacterium ulcerans which I want to identifly plasmids as well as visualize them in a circular function. I would be grateful if you can recommend some pipelines to do that. Thanks
from recycler.
It sounds like you could use a plasmid sequence classifier such as our tool PlasClass, however it has not been tested on long reads. There may be some tools that are specifically for classifying long reads as plasmids.
For visualization you can try the tool called Bandage.
from recycler.
Hi @dpellow. I used SCAPP to predict plasmids from oxford nanopore draft assembly. It turns out that it was able to make an a good prediction. I blasted the contigs with high proba values and I got a hit from BLAST.
Kudos to the SCAPP team
from recycler.
Great to hear that it worked on 3rd gen sequencing technology! Thanks for letting us know.
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Related Issues (20)
- make_fasta_from_fastg.py: error: argument -b/--bam is required HOT 1
- test HOT 1
- make_fasta_from_fastg.py :: incorrect help message HOT 1
- RuntimeError: dictionary changed size during iteration HOT 2
- ImportError: No module named recyclelib.utils HOT 1
- RuntimeWarning: invalid value encountered in sqrt HOT 5
- ZeroDivisionError: float division by zero HOT 2
- Support for assembly graphs in .gfa format HOT 3
- Recycler with Bowtie2 and MEGAHIT HOT 1
- Length of circular contigs HOT 6
- ''Node not found'' issue HOT 1
- Support for GFA graph format?
- Empty output files HOT 1
- not an issue: small suggestion for recycler.py
- recycler.py doesn't end (metagenome data) HOT 3
- No output produced HOT 3
- Visualizing the predicted plasmids HOT 1
- AttributeError: Digraph object HOT 1
- Samtools sort changed HOT 1
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