nf-core/pacvar: a pipeline for analyzing longread PacBio whole genome and repeat expansion sequencing data.

Abstract

Motivation: Pacific Biosciences (PacBio) single molecule, long-read sequencing enables whole genome annotation and the characterization of 20 complex repetitive repeat regions especially relevant to neurodegenerative diseases through their PureTarget panel. Long-read whole genome sequencing (WGS) also allows for the detection of structural variants that would be difficult to detect with traditional short-read sequencing. However, the raw unaligned Binary Alignment Map (BAM) data needs to be processed before analysis. There is a need for an intuitive comprehensive bioinformatic pipeline that can analyze this data.

Results: We present nf-core/pacvar, a comprehensive pipeline for analyzing both PacBio single-molecule PureTarget and WGS data that demultiplexes and parallelizes pre-processing, variant calling and repeat characterization. nf-core/pacvar is compatible with little configuration and has few dependencies. This pipeline enables rapid end-to-end, parallel processing of PacBio single-molecule whole genome and targeted repeat expansion sequencing.

Availability: nf-core/pacvar is available on nf-core website (https://nf-co.re/pacvar/) and on github (https://github.com/nf-core/pacvar) under MIT License (DOI 10.5281/zenodo.14813048).