Luo, Ruibang, Sedlazeck, Fritz J., Darby, Charlotte A., Kelly, Stephen M., Schatz, Michael C. (November 2017) LRSim: A Linked-Reads Simulator generating insights for better genome partitioning. Computational and Structural Biotechnology Journal, 15. pp. 478-484. ISSN 2001-0370
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 at https://github.com/aquaskyline/LRSIM
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | KeywordsLinked-read Molecular barcoding Reads partitioning Phasing Reads Simulation Genome assembly 10 × Genomics |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 9 November 2017 |
| Date Deposited: | 15 Nov 2017 16:49 |
| Last Modified: | 14 Dec 2017 20:14 |
| PMCID: | PMC5711661 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/35669 |
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