Bioinformatics Engineer

Advanced Clinical; Foster City (CA); On-site; USD 120,000 - 170,000; Full time

Job summary

Advanced Group in Foster City, CA seeks a Bioinformatics Engineer to deliver telomere-to-telomere reference genomes for non-model organisms using long‑read sequencing and computational workflows. This 12‑month contract involves designing, building, and operating genome assembly workflows in collaboration with wet‑lab and computational teams.

Responsibilities include assembling high‑quality genomes with PacBio HiFi or Oxford Nanopore data, polishing, scaffolding with Hi-C data, and evaluating

Qualifications

• Proven experience in de novo genome assembly using long read sequencing (PacBio HiFi and/or Oxford Nanopore).
• Strong expertise in assembly QC, validation, and troubleshooting complex genome features.
• Proficiency in Python and/or Bash scripting within Linux environments.
• Experience with workflow management systems (Nextflow, Snakemake, or WDL).
• Hands-on experience running large-scale genomic workloads on HPC systems and AWS platforms.

Responsibilities

• Plan and design assembly strategies for non-model organisms, including data QC, genome profiling, and contamination assessment.
• Execute and optimize long read genome assemblies (e.g., hifiasm, Verkko, Flye, Canu) toward chromosome-scale and T2T quality.
• Perform polishing and consensus refinement using complementary datasets as needed.
• Resolve haplotypes and complex genome structures, including polyploid and heterozygous genomes.
• Scaffold and curate assemblies using long-range data (Hi-C/Omni-C, Strand-seq, optical maps).
• Identify and resolve assembly errors such as misjoins and gaps, documenting curation decisions.
• Evaluate genome assemblies using Merqury, BUSCO, QUAST, and read mapping approaches.
• Assess repeats, centromeres, and telomeres to guide iterative improvements.
• Build and productionize scalable pipelines using Nextflow, Snakemake, or WDL.
• Deploy workflows using Docker or Singularity, and run on on-prem HPC (Slurm, LSF) and AWS.
• Generate reports, documentation, and release packages for internal/external use.
• Collaborate with wet-lab and cross-functional teams to troubleshoot assembly challenges.

Skills

Genomics expertise

Software engineering

Problem solving

Communication

Education

PhD in Bioinformatics

Tools

Nextflow

Snakemake

WDL

Python

Bash

HPC

Job description

We are currently seeking a highly skilled Bioinformatics Engineer to join a well-known client’s team in Foster City, CA. This role will focus on delivering telomere-to-telomere (T2T) reference genomes for non-model organisms using cutting-edge long-read sequencing technologies and computational pipelines.

This is a 12-month contract opportunity where the Bioinformatics Engineer will design, build, and operate genome assembly and curation workflows while collaborating closely with wet-lab and computational teams. This role offers the opportunity to solve complex genomic challenges including polyploidy, heterozygosity, and repetitive regions, while contributing to high-impact genomic research and data releases.

RESPONSIBILITIES

Genome Assembly & Analysis

• Plan and design assembly strategies for non-model organisms, including data QC, genome profiling, and contamination assessment.
• Execute and optimize long read genome assemblies (e.g., hifiasm, Verkko, Flye, Canu) with iterative refinement toward chromosome-scale and T2T quality.
• Perform polishing and consensus refinement using complementary datasets as needed.
• Resolve haplotypes and complex genome structures, including polyploid and heterozygous genomes.

Scaffolding & Curation

• Scaffold and curate assemblies using long-range data (e.g., Hi C/Omni C, Strand seq, optical maps).
• Identify and resolve assembly errors such as misjoins and gaps, documenting curation decisions.

Quality Assessment & Benchmarking

• Evaluate genome assemblies using tools such as Merqury (k-mer spectra), BUSCO, QUAST, and read mapping approaches.
• Assess genomic features including repeats, centromeres, and telomeres to guide iterative improvements.

Workflow Development & Infrastructure

• Build and productionize scalable pipelines using Nextflow, Snakemake, or WDL.
• Deploy workflows using containerization tools such as Docker or Singularity.
• Execute large-scale genomics workflows across on-prem HPC (e.g., Slurm, LSF) and AWS environments.
• Generate comprehensive reports, documentation, and release packages for internal and external use.
• Partner with wet lab scientists and cross-functional teams to troubleshoot complex genome assembly challenges.
• Provide technical guidance and communicate findings clearly to stakeholders.

EXPERIENCE

• Proven experience in de novo genome assembly using long read sequencing (PacBio HiFi and/or Oxford Nanopore).
• Strong expertise in assembly QC, validation, and troubleshooting complex genome features.
• Proficiency in Python and/or Bash scripting within Linux environments.
• Experience with workflow management systems (Nextflow, Snakemake, or WDL).
• Hands-on experience running large-scale genomic workloads on HPC systems and AWS platforms.

Preferred:

• Experience working with non-model organisms and complex genomes.
• Expertise in achieving chromosome-scale and T2T genome assemblies.
• Experience with genome annotation and repeat analysis.
• Demonstrated contributions to reference genome releases, publications, or community datasets.

EDUCATION

• PhD in Bioinformatics, Computational Biology, Computer Science, or a related field required.

TO BE A BEST FIT, YOUR STRENGTHS MUST INCLUDE

• Strong computational and analytical skills with deep knowledge of genomics and assembly pipelines.
• Expertise in software engineering best practices, including version control (Git), testing, and documentation.
• Ability to design and optimize scalable, reproducible bioinformatics workflows.
• Strong problem-solving mindset with the ability to address complex genomic challenges.
• Excellent communication skills for collaborating across technical and non-technical teams.
• Ability to manage multiple priorities and deliver high-quality results within timelines.
• Proactive, innovative mindset with a passion for advancing genomic technologies and data integration.

• Full-time employees are also eligible for benefits options such as health coverage, life insurance, disability insurance, and 401k benefits.

At Advanced Group, our commitment to diversity and inclusion in every part of our organization is crucial to fulfilling our mission and demonstrating our REAL values. Advanced Group is committed to providing employment opportunities without regard to sex, race, color, age, national origin, religion, gender identity or expression, sexual orientation or sexual preference, pregnancy or maternity, genetic information, marital status, disability, veteran status, or any other basis protected by applicable federal, state or local law.

Advanced Group complies with federal and state disability laws and makes reasonable accommodations for applicants and candidates with disabilities. If a reasonable accommodation is needed to participate in the job application or interview process, please contact [e-mail].