Bioinformatics Scientist

Bioinformatics Engineer T2T Genome Assembly (Non-Model Organisms)

Location: Foster City CA/Hybrid (as applicable)
Duration: 12-Month Contract

We are seeking a highly skilled Bioinformatics Engineer to support the development of Telomere-to-Telomere (T2T) reference genomes for non-model organisms. This role will focus on building, optimizing, and operating long-read genome assembly and curation pipelines using PacBio HiFi and/or Oxford Nanopore sequencing data, while collaborating closely with wet-lab and computational biology teams.

Key Responsibilities

• Design and execute genome assembly strategies for non-model organisms, including data quality assessment, genome profiling, contamination screening, and sequencing recommendations.
• Perform long-read genome assemblies using tools such as Hifiasm, Verkko, Flye, and Canu, driving assemblies toward chromosome-scale and T2T-quality results.
• Resolve haplotypes and complex genome structures, including highly heterozygous and polyploid genomes, utilizing approaches such as trio binning and Hi-C/Strand-seq-assisted phasing.
• Scaffold and curate assemblies using long-range genomic data, including Hi-C, Omni-C, Strand-seq, and optical maps.
• Identify and correct assembly errors, close gaps where feasible, and document curation decisions.
• Evaluate assembly quality using tools such as Merqury, BUSCO, QUAST, k-mer analyses, and read-mapping approaches.
• Develop and maintain scalable bioinformatics workflows using Nextflow, Snakemake, or WDL.
• Deploy and manage workflows across on-premises HPC environments and AWS cloud infrastructure.
• Generate technical reports, release documentation, and data packages for internal and external stakeholders.

Required Qualifications

• PhD in Bioinformatics, Computational Biology, Computer Science, Genomics, or a related field.
• Hands-on experience with de novo genome assembly using long-read sequencing technologies (PacBio HiFi and/or Oxford Nanopore).
• Strong expertise with assembly tools such as Hifiasm, Verkko, Flye, Canu, or similar platforms.
• Experience assessing assembly quality, troubleshooting assembly issues, and improving genome completeness.
• Strong programming skills in Python and/or Bash within Linux environments.
• Experience with workflow development using Nextflow, Snakemake, or WDL.
• Experience running large-scale genomics workloads on HPC environments (Slurm, LSF, or similar).
• Familiarity with AWS cloud services and scalable genomics computing environments.
• Strong software engineering practices, including Git version control, testing, and documentation.

Preferred Qualifications

• Experience working with non-model organisms and complex genomes.
• Demonstrated success delivering chromosome-scale or T2T genome assemblies.
• Knowledge of repeat annotation, genome annotation, and evidence-driven gene annotation workflows.
• Experience with haplotype-resolved assemblies and advanced genome curation.
• Publications, preprints, reference genome releases, or contributions to community genomic resources.

Nice to Have

• RNA-Seq integration and genome annotation experience.
• Genome browser track generation and visualization experience.
• AWS Batch, HealthOmics, and S3 data management expertise.
• Excellent communication skills and ability to collaborate across multidisciplinary teams.

This is an exciting opportunity to contribute to cutting-edge genomics research and help deliver high-quality reference genomes that support scientific discovery and innovation.