Mapping samples to multiple reference fasta
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Description
Hi,
I was thinking of adapting this pipeline to take care of multiple reference genomes. Something like each sample would be aligned to different reference fasta file. Any votes for such a feature?
The input if given would be a csv file with sample_id, path_to_reference_fasta, path_to_sample_fastq
Cheers,
Rahul
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with issue #181 and inspect how the methylseq pipeline currently accepts sample and reference inputs. Consider the proposed CSV fields—sample_id, path_to_reference_fasta, and path_to_sample_fastq—and determine the scope of supporting multiple reference FASTA files per sample. Done means the requested input can drive alignment against the specified reference for each sample.
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
- 25/100