Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 17, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab563
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Funding
- National Natural Science Foundation of China [62002388, 61772557]
- NSFC-Zhejiang Joint Fund for the Integration of Industrialization and Informatization [U1909208]
- Hunan Provincial Science and Technology Program [2018wk4001]
- 111 Project [B18059]
- King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [BAS/1/1624-01, FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, REI/1/0018-01-01, REI/1/4216-01-01, REI/1/4437-01-01, REI/1/4473-01-01, URF/1/4352-01-01, REI/1/4742-01-01, URF/1/4098-01-01]
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LongRepMarker is a novel framework for precisely marking long repeats in genomes based on global de novo assembly and k-mer based multiple sequence alignment. By introducing barcode linked reads and unique k-mers, it achieves better efficiency and accuracy in identifying repeats, outperforming existing methods in experimental results.
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).
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