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SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark

Ming-Tai Chang, Yi-An Tung, Jen-Ming Chung, Hung-Fei Yao, Yun-Lung Li, Yin-Hung Lin, Yao-Ting Wang, Chien-Yu Chen, Chung-Tsai Su
doi: https://doi.org/10.1101/239962
Ming-Tai Chang
1Atgenomix, Taipei, Taiwan,
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Yi-An Tung
2Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan,
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Jen-Ming Chung
1Atgenomix, Taipei, Taiwan,
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Hung-Fei Yao
1Atgenomix, Taipei, Taiwan,
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Yun-Lung Li
1Atgenomix, Taipei, Taiwan,
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Yin-Hung Lin
3Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan,
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Yao-Ting Wang
1Atgenomix, Taipei, Taiwan,
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Chien-Yu Chen
2Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan,
4Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan,
5Education & Research Center for Bio-Industrial Automation, National Taiwan University, Taipei, Taiwan.
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Chung-Tsai Su
1Atgenomix, Taipei, Taiwan,
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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{at}atgenomix.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 27, 2017.
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SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark
Ming-Tai Chang, Yi-An Tung, Jen-Ming Chung, Hung-Fei Yao, Yun-Lung Li, Yin-Hung Lin, Yao-Ting Wang, Chien-Yu Chen, Chung-Tsai Su
bioRxiv 239962; doi: https://doi.org/10.1101/239962
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SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark
Ming-Tai Chang, Yi-An Tung, Jen-Ming Chung, Hung-Fei Yao, Yun-Lung Li, Yin-Hung Lin, Yao-Ting Wang, Chien-Yu Chen, Chung-Tsai Su
bioRxiv 239962; doi: https://doi.org/10.1101/239962

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