custom reference genome and annotation support
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
- No merged PRs in 30d
Description
Hi!
I was wondering if there wold be support for custom genome fasta and annotation files? I see that every genome is hard coded and seems impossible to use my own genome version. Is there a work on progress for that, or would you recommend any work around for it?
Sincere regards,
Contributor guide
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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 locating where genomes and annotation files are hard coded, then determine how a user could provide custom FASTA and annotation inputs. Review the existing genome-loading entry points and tests, if present, and define done as documented support for a custom genome version and its annotations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100