Brent S Pedersen1, Aaron R Quinlan1. 1. Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.
Abstract
Motivation: Extracting biological insight from genomic data inevitably requires custom software. In many cases, this is accomplished with scripting languages, owing to their accessibility and brevity. Unfortunately, the ease of scripting languages typically comes at a substantial performance cost that is especially acute with the scale of modern genomics datasets. Results: We present hts-nim, a high-performance library written in the Nim programming language that provides a simple, scripting-like syntax without sacrificing performance. Availability and implementation: hts-nim is available at https://github.com/brentp/hts-nim and the example tools are at https://github.com/brentp/hts-nim-tools both under the MIT license.
Motivation: Extracting biological insight from genomic data inevitably requires custom software. In many cases, this is accomplished with scripting languages, owing to their accessibility and brevity. Unfortunately, the ease of scripting languages typically comes at a substantial performance cost that is especially acute with the scale of modern genomics datasets. Results: We present hts-nim, a high-performance library written in the Nim programming language that provides a simple, scripting-like syntax without sacrificing performance. Availability and implementation: hts-nim is available at https://github.com/brentp/hts-nim and the example tools are at https://github.com/brentp/hts-nim-tools both under the MIT license.
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Authors: Brent S Pedersen; Preetida J Bhetariya; Joe Brown; Stephanie N Kravitz; Gabor Marth; Randy L Jensen; Mary P Bronner; Hunter R Underhill; Aaron R Quinlan Journal: Genome Med Date: 2020-07-14 Impact factor: 11.117
Authors: Brent S Pedersen; Joe M Brown; Harriet Dashnow; Amelia D Wallace; Matt Velinder; Martin Tristani-Firouzi; Joshua D Schiffman; Tatiana Tvrdik; Rong Mao; D Hunter Best; Pinar Bayrak-Toydemir; Aaron R Quinlan Journal: NPJ Genom Med Date: 2021-07-15 Impact factor: 8.617