Investigate using only targeted references
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
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Description
Since we know which sequences we expect to see in a sample, it might be useful to only use those references for mapping. Then we could use the other references to see what we find in the unmapped sequences.
This task is to take some samples and map them with only the expected references, then compare the results with using all the references. Do we get more noise moving in with the target when we use fewer references, or do we lose more good sequences to the noise when we use all references? Is either approach significantly faster?
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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
Start by identifying the sample set and mapping entry point used by the pipeline. Run mappings with only the expected references and with all references, then compare noise in target and unmapped sequences and measure runtime. Done means the results clearly show whether either approach changes accuracy or speed significantly.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100