LRSim: A Linked-Reads Simulator generating insights for better genome partitioning
Linked-Reads provide long-range genomic information from short reads, enabling cost-effective and straightforward de novo assembly, structural variant detection, and haplotype analysis. In a new paper in Computational and Structural Biotechnology Journal, Luo et al., introduce a new software package for simulating Linked-Reads called LRSim. By imitating the library preparation and sequencing process and providing controls over workflow variants, the authors were able to make recommendations to optimize Linked-Read sequencing results.
ABSTRACT
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 on Github: https://github.com/aquaskyline/LRSIM
Read the full article in Computational and Structural Biotechnology Journal.
Linked-Reads Resources
- Genome, Exome and de novo assembly datasets
- Blog post - Everything you wanted to know about Linked-Reads
- Blog post - Get the most out of your Linked-Read data
- Data analysis software - Long Ranger and Loupe™ Genome Browser