NanoPack2: Population scale evaluation of long-read sequencing data

Abstract

SummaryIncreases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here we describe novel tools for summarizing experiments, filtering datasets and visualizing phased alignments results, as well as updates to the NanoPack software suite. Availability and implementationCramino, chopper, and phasius are written in Rust and available as executable binaries without requiring installation or managing dependencies. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows 10 Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions. Contactwouter.decoster@uantwerpen.vib.be