Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation

Abstract

MotivationWith increasing initiatives to study biodiversity through high-quality reference genomes and the growing capacity of sequencing a wide range of organisms, there is a pressing need for an accessible, reproducible, and user-friendly tool that incorporates state-of-the-art methodologies for large genome assembly. ResultsWe introduce Pipeasm, a Snakemake pipeline designed for assembling vertebrate genomes using HiFi PacBio, ONT, and HiC data. By setting a configuration file with input information and suggested parameters, Pipeasm was able to assemble multiple-sized diploid genomes ready for manual curation. Availability and ImplementationPipeasm requires an environment with Snakemake and Singularity and is available at https://github.com/itvgenomics/pipeasm.