Genomics long-read pipeline, release p1.1
phalaena:pipeline:PA-PL-genomics-longread
Variant discovery and alignment QC on long-read DNA-seq, Oxford Nanopore or PacBio HiFi. We summarise read quality with NanoPlot, align with minimap2 (Parabricks mm2-gb on the GPU branch), sort and index, call germline variants with bcftools mpileup/call, aggregate with MultiQC, and emit a canonical summary.json matching phalaena_backend/pipelines/SUMMARY_SCHEMA.md; the assistant reads this contract directly. The minimap2 preset follows the read technology: map-ont for Nanopore (paper 2.1), map-hifi for PacBio HiFi (papers 2.2 and 2.3). Pipeline ID genomics_longread. Source: phalaena_backend/pipelines/1.2_genomics_longread/. API entry: phalaena_api/app/pipelines/genomics_longread.py.
- kind
- pipeline
- status
- reviewed
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/1.2_genomics_longread
View Genomics long-read pipeline, release p1.1 on the Phalaena Wiki