Job Description

(Actual title dependent upon experience)

Universal Sequencing Technology Corporation, a biotech company headquartered in greater Boston with a branch in San Diego, is looking for a Bioinformatics software engineer to join the team. This position is a unique opportunity to work on company’s novel technology for the Next Generation Sequencing (NGS) platforms that enables many previously unachievable applications. This person will lead the development of genomic data analysis algorithms and numerical data simulation to solve challenge genomics problems in one or more of the NGS bioinformatics areas, such as haplotype phasing, structure variation detection, de novo assembly, metagenomics, and target sequencing/clinical bioinformatics as well as single cell sequencing analysis. The ideal candidate will have strong background in NGS data analysis using techniques such as sequence alignment, text indexing and searching, genome assembly, graph algorithms, combinatorial optimization and probability theory. 

In addition to strong programming skills, the candidate must have a keen interest in biology and working with real-world data. Strong interpersonal skills, a desire to understand genomics researcher needs and the ability to communicate results clearly are a must. This position will interact closely with colleagues in molecular biology.

DESIRED SKILLS:

• Strong programming experience in C/C++, Java, Python, Perl, Shell scripting.
• Strong experience with NGS DNA sequence data analysis pipelines
• Strong experience developing bioinformatics algorithms in NGS genomic data analysis
• Strong experience developing tools for numerical data analysis and simulation
• Hands on experience with NGS data analysis tools (e.g. bwa, samtools, SNP Graph, RefHap, HapCut, Bandage, etc.)
• Experience building and releasing commercial or open source software
• Experience and/or strong knowledge in cloud computing (AWS) a plus.

DUTIES AND RESPONSIBILITIES:

• Analyze internally generated sequencing data

• Work with internal and/or external biologists to understand applications and requirements

• Design and develop new data analysis pipeline processes using internally developed algorithms

• Design and develop software for applications in haplotype phasing, Structural Variation detections and de novo assembly

• Investigate and integrate open source software for use with our proprietary technologies

• Work with internal and/or external users to develop and support customized solutions based on our core products

• Actively participate in all phases of SDLC, including development, testing, bug fixing and user support.

• Write and maintain good documentations, such as, software specifications, architecture designs, testing plans and deployment plans.

• Other work and project assignments as required.

QUALIFICATIONS:

PhD in computer science, bioinformatics or related field with 0-3 years of postdoctoral experience

MSc in computer science, bioinformatics or related field with at least 5 years of post-graduate experience

Experience in any of the NGS bioinformatics areas such as haplotype phasing, structure variation detection, de novo assembly and metagenomics as well as target sequencing and clinical bioinformatics

Experience in single cell sequencing analysis is a plus.

Work well both independently and in a team environment

Ability to work in a fast-paced and quickly changing environment