SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark
Journal
bioRxiv
Date Issued
2017-12-27
Author(s)
Chang, Ming-Tai
Tung, Yi-An
Chung, Jen-Ming
Yao, Hung-Fei
Li, Yun-Lung
Lin, Yin-Hung
Wang, Yao-Ting
Su, Chung-Tsai
Abstract
Summary
SeqsLab is a platform that helps researchers to easily annotate and interpret genetic variants derived from a large quantity of personal genomes. It provides an integrated interface to annotate the variants based on curated databases as well as in silico estimation on the effects of the variants. SeqsLab adopts the scalable cluster computing framework, Spark, and incorporates several customized algorithms to speed up the process of variant annotation and interpretation. The key features of SeqsLab include efficient annotation on large structural variations, diverse combinations of variant filters, easy incorporation with a vast amount of public databases, and scalable architecture of analyzing hundreds of human whole genomes simultaneously.
Availability and Implementation
SeqsLab is implemented with JAVA. The generated annotation will then be stored in Elasticsearch for real-time query and exploratory analysis. SeqsLab can be accessed by web browsers and is freely available at http://portal.seqslab.net/.
Contact
chungtsai_su@atgenomix.com
Supplementary information
Supplementary data are available at Bioinformatics online.
Publisher
Cold Spring Harbor Laboratory
Type
journal article