{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T10:52:46Z","timestamp":1776163966146,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T00:00:00Z","timestamp":1709596800000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Academy of Finland Center of Excellence for Complex Disease Genetics","award":["352793"],"award-info":[{"award-number":["352793"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Ribotin is available on https:\/\/github.com\/maickrau\/ribotin and as a package on bioconda.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae124","type":"journal-article","created":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T11:34:50Z","timestamp":1709638490000},"source":"Crossref","is-referenced-by-count":14,"title":["Ribotin: automated assembly and phasing of rDNA morphs"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2971-267X","authenticated-orcid":false,"given":"Mikko","family":"Rautiainen","sequence":"first","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki , Helsinki,","place":["Finland"]}]}],"member":"286","published-online":{"date-parts":[[2024,3,5]]},"reference":[{"key":"2026041222493336100_btae124-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2026041222493336100_btae124-B3","doi-asserted-by":"crossref","first-page":"a006742","DOI":"10.1101\/cshperspect.a006742","article-title":"The RNA worlds in context","volume":"4","author":"Cech","year":"2012","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2026041222493336100_btae124-B4","article-title":"Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double 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of diploid chromosomes with verkko","volume":"41","author":"Rautiainen","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2026041222493336100_btae124-B17","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/s13059-020-02157-2","article-title":"GraphAligner: rapid and versatile sequence-to-graph alignment","volume":"21","author":"Rautiainen","year":"2020","journal-title":"Genome Biol"},{"key":"2026041222493336100_btae124-B18","doi-asserted-by":"crossref","first-page":"2476","DOI":"10.1093\/bioinformatics\/btab004","article-title":"MBG: minimizer-based sparse de Bruijn graph construction","volume":"37","author":"Rautiainen","year":"2020","journal-title":"Bioinformatics"},{"key":"2026041222493336100_btae124-B19","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.gpb.2021.08.003","article-title":"High-quality Arabidopsis thaliana genome assembly with nanopore and HiFi long reads","volume":"20","author":"Wang","year":"2022","journal-title":"Genomics Proteomics 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