HTSlib-js: Developer toolkit for a client-side JavaScript interface for HTSlib

Background: An increasing number of bioinformatics tools are developed in JavaScript to provide an interactive visual interface to users. However, there are no tools yet that enable fast client-side analysis of large, high-throughput sequencing file formats, such as BAM and VCF files. Results: We pr...

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Bibliographic Details
Published in:	bioRxiv
Main Authors:	Park, Jeongbin, Childs, Liam H, Schlesner, Matthias, Eils, Roland
Format:	Paper
Language:	English
Published:	Cold Spring Harbor Cold Spring Harbor Laboratory Press 27.08.2018 Cold Spring Harbor Laboratory
Edition:	1.1
Subjects:	Bioinformatics Next-generation sequencing Software reviews browser-based applications interactive data visualization and analysis high-throughput sequencing JavaScript
ISSN:	2692-8205, 2692-8205
Online Access:	Get full text
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Summary:	Background: An increasing number of bioinformatics tools are developed in JavaScript to provide an interactive visual interface to users. However, there are no tools yet that enable fast client-side analysis of large, high-throughput sequencing file formats, such as BAM and VCF files. Results: We present HTSlib-js, an asm.js-based JavaScript wrapper for HTSlib, the de facto standard for processing BAM and VCF files. HTSlib-js exploits recent technological advances in web browser engines that dramatically increase the performance of browser-based tools to enable swift processing of files in the aforementioned formats. HTSlib-js enables quick development of JavaScript-based applications that include processing of aligned sequence reads and variant calling data. Conclusions: HTSlib-js constitutes a toolkit for developers to easily write fast, accessible, browser-based applications that place an emphasis on data visualization, interactivity and privacy. Real-world examples demonstrate the capabilities of HTSlib-js and serve as guide for own developments.
Bibliography:	SourceType-Working Papers-1 ObjectType-Working Paper/Pre-Print-1 content type line 50
ISSN:	2692-8205 2692-8205
DOI:	10.1101/397935