nf-core / nf-core/pairgenomealign
Produce more annotation files for the target genome.
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 12
- Forks
- 5
- Avg merge
- 1d 10h
- Merged PRs (30d)
- 6
Description
Description of feature
When browsing the multi-genome CRAM file, it may be useful to have some genomic context. But gene annotaiton files may not be available. At least, the pipeline could run tantan or windowmasker, and produce some BED files that can be loaded in the IGV. In addition, it could also run the self-alignment of the target to itself, and produce a coverage plot, that would allow to see the shadow of repeats and duplications.
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
No files, tests, or entry points are named. First clarify how the pipeline should invoke tantan or windowmasker, create BED files for IGV, run target self-alignment, and produce the coverage plot; the work is done when these outputs are generated and can be loaded or viewed as described.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100