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pacsomatic

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About pacsomatic

P

pacsomatic

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi

pacsomatic is an agent skill for preparing and launching the nf-core pacsomatic workflow, which analyses matched tumour and normal PacBio HiFi genomics data from unaligned BAM files. The skill includes a helper script that prepares one matched tumour and normal pair, generates a samplesheet and reproducible launch files, and then runs the Nextflow driver locally or submits it to a scheduler. The pipeline realigns the input BAM files, and the helper is for unaligned HiFi BAMs and optional PacBio index files. The skill warns against substituting short-read data, and against treating a BAM file name as evidence of the platform, the matched identity or methylation information. The reviewed upstream development commit is pinned by default. GitHub had no releases or tags on 1 October 2026, even though an internal manifest names version 1.0.0, so the helper pins the commit and does not invent a release tag. The skill describes its workflow as a development workflow that has been reviewed against source, not a clinically validated assay. Its guide records the sources and the scientific checks. Use it for research on matched cancer genomes sequenced with PacBio HiFi.

View pacsomaticAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/pacsomatic