Consider adding a low-complexity sequence masking to genomes before building
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- Dominant language
- Nextflow
- Stars
- 22
- Forks
- 13
- Avg merge
- 8d 5h
- Merged PRs (30d)
- 3
Description
Description of feature
This can in some cases improve classification as it doesn't try to find the best place for unspecific reads (assuming a tool accepts such masked genomes).
It may also make databases smaller as it will remove reundant unspecific regions (e.g. by reducing the number of kmers)
E.g. with dustmasker
Idea from: https://github.com/khyox/recentrifuge/wiki/Centrifuge-nt#step-by-step-instructions
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 in the issue. Start by locating the database-building step and reviewing how genomes are prepared before building; evaluate whether dustmasker is suitable for optional low-complexity masking. Done should include a defined masking workflow and clear evidence of its effect on classification and database size.
Written by the indexing model from the issue text.
Assessment
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100