Abstract
BackgroundRepetitive sequences account for a large proportion of eukaryotes genomes. Identification of repetitive sequences plays a significant role in many applications, such as structural variation detection and genome assembly. Many existing de novo repeat identification pipelines or tools make use of assembly of the high-frequency k-mers to obtain repeats. However, a certain degree of sequence coverage is required for assemblers to get the desired assemblies. On the other hand, assemblers cut the reads into shorter k-mers for assembly, which may destroy the structure of the repetitive regions. For the above reasons, it is difficult to obtain complete and accurate repetitive regions in the genome by using existing tools.ResultsIn this study, we present a new method called RepAHR for de novo repeat identification by assembly of the high-frequency reads. Firstly, RepAHR scans next-generation sequencing (NGS) reads to find the high-frequency k-mers. Secondly, RepAHR filters the high-frequency reads from whole NGS reads according to certain rules based on the high-frequency k-mer. Finally, the high-frequency reads are assembled to generate repeats by using SPAdes, which is considered as an outstanding genome assembler with NGS sequences.ConlusionsWe test RepAHR on five data sets, and the experimental results show that RepAHR outperforms RepARK and REPdenovo for detecting repeats in terms of N50, reference alignment ratio, coverage ratio of reference, mask ratio of Repbase and some other metrics.
Highlights
Repetitive sequences account for a large proportion of eukaryotes genomes
Conlusions: We test RepAHR on five data sets, and the experimental results show that RepAHR outperforms RepARK and REPdenovo for detecting repeats in terms of N50, reference alignment ratio, coverage ratio of reference, mask ratio of Repbase and some other metrics
We evaluate the repeats identified by RepAHR, RepARK and REPdenovo on five next-gen‐ eration sequencing (NGS) data sets
Summary
Identification of repetitive sequences plays a significant role in many appli‐ cations, such as structural variation detection and genome assembly. Many existing de novo repeat identification pipelines or tools make use of assembly of the highfrequency k-mers to obtain repeats. The repetitive sequences are patterns of nucleic acids, which occur multiple times in genome with the same or approximate form. Based on their structure and distribution in the genome, repetitive sequences are classified into several types, i.e. tandem repeats, interspersed repeats and so on. Transposable elements account for a large fraction of the genome and have influence on much of the mass of DNA in eukaryotic genomes [1]. For many basic analysis methods of genome sequences, such as de novo assembly, sequence alignment, sequence error correction, etc., repetitive sequences pose a challenge to these tasks [5]
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