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

Although high-quality chromosome-scale genome assemblies are feasible, assembling large ones remains complex and resource-intensive. This demands reproducible and automated workflows that not only implement current best practices efficiently but also allow for improvement alongside future updates to those standards.

We present Pipeasm, a Snakemake-based genome assembly pipeline containerized with Singularity. Pipeasm can use HiFi, ONT, and Hi-C data, automating read trimming, nuclear and mitogenome assembly, scaffolding, decontamination, and quality evaluation. Applied to four vertebrate species with distinct genomic characteristics, starting from a single command line and configuration file, it produced assemblies with scaffold L50 proportional to the expected chromosome and genome length, and up to 99.6% BUSCO completeness. Its output also includes detailed reports for each step, genome statistics, Hi-C maps, and files ready for curation.

Pipeasm is available at https://github.com/itvgenomics/pipeasm, implemented in Python/Snakemake with Singularity, and runs on Unix-based systems.