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bioRxiv · 10.1101/2024.10.21.598381

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

Silva, B. M.·Trindade, F. d. J.·Canesin, L. E. C.·Souza, G. B. S.·Aleixo, A.·Nunes, G. L.·Oliveira, R. R. M.
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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.

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Silva, B. M., Trindade, F. d. J., Canesin, L. E. C., Souza, G. B. S., Aleixo, A., Nunes, G. L., Oliveira, R. R. M.. 2024-10-24. Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation. https://doi.org/10.1101/2024.10.21.598381

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