Nextflow pipeline for PacBio data

A Nextflow pipeline using PacBio long-read sequencing data

Purpose

• Vector and plasmid characterization

Main components

• Basic QC on input reads
• Alignment to a user-supplied reference, a human reference (T2T), and helper and rep-cap plasmids with pbmm2
• Methylation quantification at CpG sites with primrose
• Call variants (lofreq, pbsv) and produce variation table for each reference locus
• Truncation hotspot (read start and end positions) and read length figures
• Chimeric reads detection using Alvis
• Generate positional sequence quality metrics
• Figures, tables, and downloads provided in report on RStudio Connect

Input

• Unaligned bam of ccs reads
• Reference FASTA
• Various optional control and metadata parameters