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. 2018 Oct 1;34(19):3387-3389.
doi: 10.1093/bioinformatics/bty358.

hts-nim: scripting high-performance genomic analyses

Brent S Pedersen  1 , Aaron R Quinlan  1
Affiliations

hts-nim: scripting high-performance genomic analyses

Brent S Pedersen et al. Bioinformatics. .

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.

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