RT Journal Article
SR Electronic
T1 BasePlayer: Versatile Analysis Software for Large-scale Genomic Variant Discovery
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 126482
DO 10.1101/126482
A1 Riku Katainen
A1 Iikki Donner
A1 Tatiana Cajuso
A1 Eevi Kaasinen
A1 Kimmo Palin
A1 Veli Mäkinen
A1 Lauri A. Aaltonen
A1 Esa Pitkänen
YR 2017
UL http://biorxiv.org/content/early/2017/04/11/126482.abstract
AB Next-generation sequencing (NGS) is being routinely applied in life sciences and clinical practice, where the interpretation of the resulting massive data has become a critical challenge. Computational workflows, such as the Broad GATK, have been established to take raw sequencing data and produce processed data for downstream analyses. Consequently, results of these computationally demanding workflows, consisting of e.g. sequence alignment and variant calling, are increasingly being provided for customers by sequencing and bioinformatics facilities. However, downstream variant analysis, whole-genome level in particular, has been lacking a multi-purpose tool, which could take advantage of rapidly growing genomic information and integrate genetic variant, sequence, genomic annotation and regulatory (e.g. ENCODE) data interactively and in a visual fashion. Here we introduce a highly efficient and user-friendly software, BasePlayer (http://baseplayer.fi), for biological discovery in large-scale NGS data. BasePlayer enables tightly integrated comparative variant analysis and visualization of thousands of NGS data samples and millions of variants, with numerous applications in disease, regulatory and population genomics. Although BasePlayer has been designed primarily for whole-genome and exome sequencing data, it is well-suited to various study settings, diseases and organisms by supporting standard and upcoming file formats. BasePlayer transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.