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Comput Struct Biotechnol J. 2017 Nov 9;15:478-484. doi: 10.1016/j.csbj.2017.10.002. eCollection 2017.

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning.

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Department of Computer Science, Johns Hopkins University, United States.
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, United States.
Center for Health Informatics and Bioinformatics, New York University School of Medicine, United States.
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, United States.


Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclude from the phasing and assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing genomes of different sizes and complexities. These optimizations improve results by orders of magnitude, and enable the development of novel methods. LRSim is available at


10X Genomics; Genome assembly; Linked-read; Molecular barcoding; Phasing; Reads partitioning; Reads simulation

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