A sensitive repeat identification framework based on short and long reads

Abstract

Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).

The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments

“…Although it is routine that the identification and masking of repeats are performed before the gene prediction, repeat identification tools available at present can not totally find and mask all the repeats. 37 This is exactly the case for the YHSC genome with a high proportion of repeats. In this study, 24 of the 173 expanded domains exist in transposon-encoded proteins ( Table S11 ).…”

Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

“…Thorough annotation of TEs is ideal for dealing with the deluge of genome data. Therefore, de novo repeat identification was performed by Repeat Modeller2 ( Flynn et al, 2020 ), LongRepMarker ( Liao et al, 2021 ), and Extensive De Novo TE Annotator (EDTA) ( Ou et al, 2019 ). The unclassified repeats were further classified using DeepTE ( Yan et al, 2020 ).…”

msRepDB: a comprehensive repetitive sequence database of over 80 000 species

“…Generation of the multi-alignment unique k-mers and their coverage regions on overlap sequences . The multi-alignment unique k-mers were first proposed in the paper of LongRepMarker ( 24 ), which refers to the unique k-mers that can be aligned to multiple different locations in the overlap sequences. Due to the sequencing bias, the high frequency threshold is often difficult to obtain accurately, which has a great impact on the range of the high frequency k-mers ( 29–31 ).…”

“…LongRepMarker ( 24 ) is a new framework developed recently by our group for comprehensive identification of genomic repetitive sequences. Comprehensive evaluations carried out in the study of LongRepMarker not only show that LongRepMarker can achieve more satisfactory results than the existing detection methods, but can also discover a large number of new repeat sequences and families.…”