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Scientist NGS

San Francisco Metro Area, California

Post Date: 09/26/2017 Job ID: JN -092017-20097
Seeking a scientist to join a vibrant interdisciplinary group of scientists to develop and facilitate interpretation complex next-generation sequencing data of various tumor xenografts and derived single-cells.

Responsibilities include, but are not limited to:
Adapt open source tools or develop visualization methods to enable bench scientists to query, display and interpret NGS data types. These include RNA-expression from single-cells and bulk tissues, variant data from exome sequencing, copy-number data from whole genome sequencing, and epigenetic data.
Manage the development of a single cell RNAseq data viewer application in a cloud-based architecture for internal and external collaborators.
Integrate a sequencing LIMs (Clarity) for our CQR Illumina sequencers
Maintain existing databases for workflow (OWL), sequencing results, and PCR-primers. Initiate integration of sequencing results database with Clarity LIMs.
Facilitate data sharing/management from internal and open-source based databases.

Skills/Knowledge:
Proficiency in shell, Python, R/Shiny/R Connect, PostGreSQL, MySQL, Perl. Javascript or PHP considered a plus.
Comfortable in a linux and docker environment.
Familiar with NGS technologies, single-cell technologies, sequence analysis tools and public visualization resources.
Experience with Amazon EC2 cloud resources; e.g. S3, EC2, Lambda and others.
Highly self-motivated and enjoy working as part of a multi-disciplinary team
Outstanding oral and written communication skills
Detail-oriented

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