TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.

ABSTRACT: Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomer

SUBMITTER: Novak P 

PROVIDER: S-EPMC5499541 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature