A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes

High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide...

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Bibliographic Details
Published in:Plants (Basel) 2022-08, Vol.11 (16), p.2103
Main Authors: Kirov, Ilya, Kolganova, Elizaveta, Dudnikov, Maxim, Yurkevich, Olga Yu, Amosova, Alexandra V, Muravenko, Olga V
Format: Article
Language:English
Subjects:
Algorithms
Annotations
Arrays
Assembly
Bioinformatics
Cell division
Chromosomes
Conserved sequence
Cytogenetics
Deoxyribonucleic acid
DNA
DNA sequencing
Evolution
Gene expression
Gene mapping
Gene sequencing
genome
Genomes
Identification
Identification and classification
Methods
Monomers
Nanopore sequencing
Nucleotide sequence
Nucleotide sequencing
pipeline
Plant genetics
Satellite DNA
Software
tandem repeats
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Summary:High-copy tandemly organized repeats (TRs), or satellite DNA, is an important but still enigmatic component of eukaryotic genomes. TRs comprise arrays of multi-copy and highly similar tandem repeats, which makes the elucidation of TRs a very challenging task. Oxford Nanopore sequencing data provide a valuable source of information on TR organization at the single molecule level. However, bioinformatics tools for de novo identification of TRs in raw Nanopore data have not been reported so far. We developed NanoTRF, a new python pipeline for TR repeat identification, characterization and consensus monomer sequence assembly. This new pipeline requires only a raw Nanopore read file from low-depth (
ISSN:2223-7747
2223-7747
DOI:10.3390/plants11162103