Bioinformatics Engineer II

Ambry Genetics; United States; On-site; USD 90,000 - 140,000; Full time

Job summary

Ambry Genetics seeks a software engineer to design and implement bioinformatics tools, driving end-to-end solutions from ideation to release. You will collaborate with clients, product owners, and stakeholders to clarify workflows and requirements, and contribute to robust software with a focus on clean code and scalable design.

Responsibilities include mentoring junior engineers, participating in code reviews, and ensuring high-quality documentation, testing, and deployment practices in Linux

Qualifications

• Bachelor's degree (or higher) in Bioinformatics, CS or related field with 5+ years of work experience.
• Proficient in Python coding.
• Linux environments: compiling from source & text manipulations with pipes.
• Relational databases experience (MySQL, PostgreSQL, SQL Server).
• Git, unit testing, and documentation proficiency.
• Knowledge of next-generation sequencing data formats (FASTQ, BAM, VCF, GTF).
• Excellent communication and interpersonal skills.

Responsibilities

• Drive technical solutions end-to-end from ideation to release.
• Design and develop custom software according to ticket specifications.
• Mentor engineers and set standards for excellence.

Skills

Python

Linux

Relational databases

Git

Unit testing

Documentation

Bioinformatics formats

Education

Bachelor's / Master’s / PhD in Bioinformatics or CS

Tools

Docker

APIs

CI/CD

Job description

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.

Compensation

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

Qualifications

• Bachelor's degree (+ at least 5 years work experience), Master’s 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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