Bioinformatics Engineer II

Ambry Genetics; California (MO); On-site; USD 90,000 - 140,000; Full time

Job summary

Ambry Genetics is seeking a skilled software engineer to drive end-to-end solutions for sequencing workflows. You will design and develop software from ticket specifications, mentor junior engineers, and collaborate with clients and product owners.

Required: Python proficiency, Linux experience, and solid knowledge of relational databases. Familiarity with NGS data formats and software engineering practices (Git, testing, and documentation) is expected.

Qualifications

• Bachelor's degree with 5+ years of experience, or higher degrees.
• Strong Python programming skills.
• Linux OS proficiency and shell scripting.
• Relational databases experience (MySQL, PostgreSQL, MS SQL Server).
• Software engineering best practices (Git, unit tests, and documentation).
• Familiarity with NGS data formats (FASTQ, BAM, VCF) is a plus.

Responsibilities

• Drive technical solutions end-to-end from ideation to release.
• Design and develop software according to ticket specifications.
• Mentor junior engineers and set coding standards.
• Provide feedback on code reviews.
• Meet with clients, product owners, and stakeholders to clarify workflows.
• Identify and resolve blockers during development.
• Monitor processes and troubleshoot issues.
• Other duties as assigned.

Skills

Python

Linux

Git

Unit testing

Documentation

Communication

Education

Bachelor's degree (+5 years) or higher

Tools

MySQL

PostgreSQL

MS SQL Server

Git

Docker

Job description

Compensation

Pay Range: $90,000 - $140,000 USD

Essential Functions

• Drive technical solutions to problems, including end-to-end process flow from ideation to release, and estimating time and complexity
• Design and develop custom software according to ticket specifications
• Act as a role model for the team, settings standards for excellence and mentoring junior engineers
• Provide clear and consistent feedback on code reviews
• Meet with clients, partners, product owners, or other stakeholders to understand and clarify workflows and requirements
• Highlight blockers or issues arising during development to resolve in a timely manner
• Monitor process and log information, troubleshooting issues as needed
• Other duties as assigned.

Qualifications

• Bachelor\'s degree (+ at least 5 years work experience), Master\u2019s degree (+ at least 2 years work experience), or PhD degree in Bioinformatics, Computer Science, or a related field
• Proficient in Python coding
• Intermediate-to-advanced experience working in Linux environments (e.g. compiling programs from source, performing text manipulations with pipes)
• Intermediate-to-advanced experience in relational databases (e.g., MySQL, PostgreSQL, Microsoft SQL Server)
• Proficiency with software engineering best practices, including git version control, unit testing, and documentation
• Knowledge of next-generation sequencing technologies and standard bioinformatics data formats (e.g., FASTQ, BAM, VCF, GTF)
• Excellent communication and interpersonal skills.

Preferred

• Experience with cloud computing environment (AWS, Azure, Google Cloud)
• Familiarity with Atlassian suite applications (Jira, Confluence, BitBucket)
• Knowledge of clinical genetics databases (e.g., Clinvar, HGMD) and HGVS sequence variant nomenclatures
• Prior experience in biology and/or an understanding of mutation analysis
• Creating and developing Docker containers
• Experience developing APIs
• Experience with CI/CD (e.g. Bamboo, Jenkins, AWS Code Pipeline)

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