Ribotin: Automated Assembly and Phasing of RDNA Morphs

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2024 Mar 5

PMID 38441320

Authors

Mikko Rautiainen

Affiliations

Soon will be listed here.

Abstract

Motivation: The ribosomal DNA (rDNA) arrays are highly repetitive and homogenous regions which exist in all life. Due to their repetitiveness, current assembly methods do not fully assemble the rDNA arrays in humans and many other eukaryotes, and so variation within the rDNA arrays cannot be effectively studied.

Results: Here, we present the tool ribotin to assemble full length rDNA copies, or morphs. Ribotin uses a combination of highly accurate long reads and extremely long nanopore reads to resolve the variation between rDNA morphs. We show that ribotin successfully recovers the most abundant morphs in human and nonhuman genomes. We also find that genome wide consensus sequences of the rDNA arrays frequently produce a mosaic sequence that does not exist in the genome.

Availability And Implementation: Ribotin is available on https://github.com/maickrau/ribotin and as a package on bioconda.

Citing Articles

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike K Genome Res. 2024; 34(11):1919-1930.

PMID: 39505490 PMC: 11610574. DOI: 10.1101/gr.279334.124.

Epigenetic control and inheritance of rDNA arrays.

Potapova T, Kostos P, McKinney S, Borchers M, Haug J, Guarracino A bioRxiv. 2024; .

PMID: 39372739 PMC: 11451732. DOI: 10.1101/2024.09.13.612795.

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike K bioRxiv. 2024; .

PMID: 38529488 PMC: 10962732. DOI: 10.1101/2024.03.15.585294.

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