nf-core / nf-core/genomeassembler
Read phasing?
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- Nextflow
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Description
Description of feature
Currently genomeassembler does not assemble phased genomes. Clearly, being able to produce phased assemblies would be neat. There are several phasing strategies, for example hifiasm would support HI-C reads, or parental short-reads.
Maybe using https://github.com/yangao07/longcallD to phase the long-reads (assuming a reference is available) pre-assembly and assembling haplotypes from the phased reads would be a alternative option, that requires no additional inputs?
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 comparing the proposed phasing strategies: Hi-C or parental short reads via hifiasm, and long-read phasing with longcallD when a reference is available. Clarify the required inputs and expected phased-assembly outputs before implementation; done means genomeassembler can produce phased assemblies through a defined strategy.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100