nf-core / nf-core/funcprofiler
Decide whether to support long-reads
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- Dominant language
- Nextflow
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- 2d 23m
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- 1
Description
Description of feature
Should funcprofiler support long reads? This is open for discussion but I'm leaning towards "no". I have a hard time believing that read-based tools will outperform assembly-based approaches for long reads, but I'm happy to be proven wrong. If you want to see read-based long-read tools supported, please comment below with the tools and how data gets processed for them (eg does it take raw/trimmed reads? Do you fragment the reads into and profile from those "short read" fragments?) Version 1.0 will likely just support short reads but if there is sufficient interest we can set a target for a future release.
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 reviewing the issue discussion and the repository's current short-read workflow. Investigate candidate read-based long-read tools, including whether they consume raw or trimmed reads or fragmented reads; done means documenting a support decision and, if appropriate, a target for a future release.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100