nf-core / nf-core/seqinspector
Enable unaligned BAM (uBAM) input
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 28
- Forks
- 44
- Avg merge
- 11d 8h
- Merged PRs (30d)
- 2
Description
Description of feature
Long reads from ONT or PacBio are typically stored as unaligned BAM (uBAM) files, so it would be beneficial to enable uBAM input. Some tools already accept BAM input e.g. sequali, FastQC and ToulligQQ, but for others a uBAM to FASTQ conversion would be required.
uBAM often come with additional metadata that could be valuable for QC. This includes both run information e.g. read start time for ONT and methylation information (MM/ML tag) for each read which is missing from the FASTQs that would enable read methylation QC, for example using modkit.
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. Start by tracing how the Nextflow pipeline accepts sequencing inputs and how each QC tool handles BAM or FASTQ; determine which tools can consume uBAM directly and where conversion or metadata preservation is needed. Done means the supported uBAM workflow and its QC coverage are defined and tested.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100