pipelines-docs
Long-Read PacBio HiFi
The long-read alignment pipeline for PacBio HiFi data is designed for per-sample and per-library execution, handling one or multiple unaligned BAM files. The pipeline is optimized for distributed processing, requiring each unaligned BAM file to correspond to a single SMRT Cell.
Key Pipeline Steps
- Alignment with pbmm2: Initial alignment of the raw reads to the reference genome using pbmm2.
- Read Groups Assignment: Assignment of reads to specific groups.
- Methylation and Tags Linking: Linking the methylation status information and other specific tags from the unaligned to the alignment BAM file.
Pipeline Chart
