“The survival ... of certain favored words in the struggle for existence is natural selection,” - Charles Robert Darwin. □ Ages and cycle...
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Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve 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.