bio-alignment-amplicon-clipping skillA
bio-alignment-amplicon-clipping is agent-read markdown (skill) from pku-yuangroup/openai4s: Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints..
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What the file says
## Version Compatibility Reference examples tested with: samtools 1.19+, pysam 0.22+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Alignment Amplicon Clipping **"Trim primer-derived bases from amplicon BAM"** -> Soft- or hard-clip the 5' primer footprint after alignment using a primer BED, then repair fixmate/MD/NM tags. - CLI: `samtools ampliconclip -b primers.bed input.bam -o clipped.bam` (since samtools 1.11) - Alternative: `iVar trim`, `BAMClipper`, `fgbio ClipBam` ## Why Primer Trimming After Alignment Amplicon panels (SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, fusion panels, 16S rRNA) use designed PCR primers for enrichment. Primer-derived bases at read 5' ends do NOT reflect biological sequence -- they reflect the primer template. Without trimming: - False reference confirmation at primer footprint positions. …
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How to install
mdr add pku-yuangroup/openai4s/bio-alignment-amplicon-clipping@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-amplicon-clipping@sha256:0f46a3c50274568aPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_2ddegio24prwdafz)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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