New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

Author:

Gonzalez-Garcia Laura1,Guevara-Barrientos David1,Lozano-Arce Daniela1,Gil Juanita2,Díaz-Riaño Jorge1,Duarte Erick1,Andrade Germán1,Bojacá Juan Camilo1,Hoyos-Sanchez Maria Camila1,Chavarro Christian1,Guayazan Natalia3,Chica Luis Alberto45,Buitrago Acosta Maria Camila1,Bautista Edwin1,Trujillo Miller1,Duitama Jorge1ORCID

Affiliation:

1. Systems and Computing Engineering Department, Universidad de los Andes

2. Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, USA

3. Department of Biological Sciences, Universidad de los Andes

4. Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes

5. Max Planck Tandem Group in Computational Biology, Universidad de los Andes

Abstract

Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.

Funder

Ministerio de Ciencia Tecnologia e Innovacion, Colombia

Universidad de los Andes

Publisher

Life Science Alliance, LLC

Subject

Health, Toxicology and Mutagenesis,Plant Science,Biochemistry, Genetics and Molecular Biology (miscellaneous),Ecology

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