hts-nim: scripting high-performance genomic analyses

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...

Full description

Saved in:
Bibliographic Details
Published inBioinformatics Vol. 34; no. 19; pp. 3387 - 3389
Main Authors Pedersen, Brent S, Quinlan, Aaron R
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.10.2018
Subjects
Applications Notes
Computational Biology
Genomics
Programming Languages
Software
Online AccessGet full text

Cover

More Information
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bty358