gfa file to visualize the final consensus fasta by Bandage
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 348
- Forks
- 31
- PR merge metrics
- No merged PRs in 30d
Description
Hi Ryan,
I am using Trycycler to assembly 90 bacterial genomes from fish guts. It is an amazing and very helpful tool. I was able to obtain circular, > 98 % completeness, and very good coverage in all the genomes after following the pipeline and polishing the assemblies by medaka. However, I'm wondering if there is an easy and proper way to obtain a gfa-like file to visualize the genomes in bandage. I would like to plot those circular chromosomes and plasmids as well as those linear ones in a bandage-like figure. I've been looking if there is any available script in the Trycycler pipeline to do this, but so far I haven't found any.
Hope you can help me.
Thank you in advance.
Arturo.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing how the Trycycler pipeline produces its final consensus FASTA and whether its existing scripts expose graph information. Determine how circular chromosomes, plasmids, and linear sequences should be represented, then verify that the resulting GFA-like output can be opened and visualized in Bandage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100