gbouras13 / gbouras13/plassembler
Multiple chromosomes - combined reference for even copy number distribution
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 90
- Forks
- 12
- Avg merge
- 6d 4h
- Merged PRs (30d)
- 2
Description
For bacteria with multiple chromosomes, perhaps calculate plasmid copy number based off the combined chromosomal contigs, not just the first one.
Contributor guide
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 the plasmid copy-number calculation and the code that selects chromosomal contigs. Determine how multiple chromosomes are represented and how combined coverage should affect even copy-number distributions. Done means the calculation uses all relevant chromosomal contigs for multi-chromosome bacteria without changing single-chromosome behavior; the issue names no files or tests to run.
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
- 35/100