Ribotin: automated assembly and phasing of rDNA morphs.
Bioinformatics
; 40(3)2024 03 04.
Article
in En
| MEDLINE
| ID: mdl-38441320
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Genome
Limits:
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2024
Document type:
Article
Affiliation country:
Finland
Country of publication:
United kingdom