ArticleBioinformatics (Oxford, England)2024
Ribotin: automated assembly and phasing of rDNA morphs.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 13 citations in OpenAlex.
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- Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs.bioRxiv : the preprint server for biology · 2026Article
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- Human acrocentric chromosome short armbioRxiv : the preprint server for biology · 2025Article
- Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.Cell genomics · 2025Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
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- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.bioRxiv : the preprint server for biology · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.Genome research · 2024Article
- Epigenetic control and inheritance of rDNA arrays.bioRxiv : the preprint server for biology · 2024Article
- Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe 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.
resultsHere, 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.