RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.
TAREAN (TAndem REpeat ANalyzer) is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J.
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Nucleic Acids Res. 2017 Jul 7;45(12):e111. doi: 10.1093/nar/gkx257. PMID: 28402514; PMCID: PMC5499541.
Novák P, Neumann P, Macas J.
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
Nat Protoc. 2020 Nov;15(11):3745-3776. doi: 10.1038/s41596-020-0400-y. Epub 2020 Oct 23. PMID: 33097925.