Time- and memory-efficient genome assembly with Raven.

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Robert Vaser, Mile Šikić

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Robert Vaser: Laboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia. ORCID
Mile Šikić: Laboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia. mile_sikic@gis.a-star.edu.sg. ORCID

PMID: 38217213 DOI: 10.1038/s43588-021-00073-4

Whole genome sequencing technologies are unable to invariably read DNA molecules intact, a shortcoming that assemblers try to resolve by stitching the obtained fragments back together. Here, we present methods for the improvement of de novo genome assembly from erroneous long reads incorporated into a tool called Raven. Raven maintains similar performance for various genomes and has accuracy on par with other assemblers that support third-generation sequencing data. It is one of the fastest options while having the lowest memory consumption on the majority of benchmarked datasets.

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Vaser, R. & Sikic, M. 2021. Assemblies generated in the manuscript ‘Time and memory efficient genome assembly with Raven’. Zenodo https://doi.org/10.5281/zenodo.4443062
Vaser, R. & Sikic, M. 2021. Raven source code used in the manuscript ‘Time and memory efficient genome assembly with Raven’. Zenodo https://doi.org/10.5281/zenodo.4672196

IP-2018-01-5886/Hrvatska Zaklada za Znanost (Croatian Science Foundation)
KK.01.1.1.01.0009/EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)

Journal Article

OpenLB
Open Library of Bioscience