If performance is an issue, could transition to nvbowtie (GPU) ?
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question
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Came across an implementation of bowtie 2 for nvidia GPU's
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
Read the linked nvbowtie implementation and inspect how MiCall currently performs its FASTQ processing and alignment work. Determine whether a GPU transition is technically and operationally feasible; done means a defined migration scope, compatibility assessment, and agreed implementation plan.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100