Bioinformatics Engineer

Overview

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.

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) 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.
• 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.
• Deliver haplotype-resolved assemblies where required.
• 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.
• 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.
• Familiarity with RNA-seq integration and genome browser track development.
• Demonstrated contributions to reference genome releases, publications, or community datasets.

Education

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

Qualifications

• 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.

Benefits

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