Bioinformatics Engineer -- T2T Genome Assembly

R&D Partners is seeking to hire a Bioinformatics Engineer — T2T Genome Assembly in Foster City, CA.

Your main responsibilities as a Bioinformatics Engineer — T2T Genome Assembly:

·      Plan assembly approaches for non model organisms (data QC, genome profiling, contamination screening, coverage targets) and advise sequencing strategy.

·      Run and iterate long read assemblies and consensus refinement (e.g., hifiasm/Verkko/Flye/Canu; polishing as appropriate) toward chromosome scale, T2T quality results.

·      Resolve haplotypes and complex ploidy/heterozygosity (e.g., trio binning; Hi C/Strand seq assisted phasing) and deliver haplotype resolved assemblies when required.

·      Scaffold and curate assemblies with long range data (e.g., Hi C/Omni C, Strand seq, optical maps): detect/resolve mis joins, close gaps where feasible, and document curation decisions.

·      Benchmark quality and completeness (e.g., k mer spectra/Merqury, BUSCO, QUAST, read mapping), including repeat/centromere/telomere assessments to guide iterative improvements.

What we are looking for in a Bioinformatics Engineer — T2T Genome Assembly:

·      PhD in bioinformatics, computational biology, computer science, or related field.

·      Proven de novo assembly experience on long reads (PacBio HiFi and/or ONT), including tuning and iterative improvement.

·      Assembly QC/validation expertise and ability to diagnose common failure modes in complex genomes.

·      Strong scripting/programming skills (Python and/or Bash) in Linux; solid software engineering practices (Git, testing, documentation).

·      Workflow + compute operations experience: Nextflow/Snakemake/WDL; running large genomics workloads on on prem HPC (e.g., Slurm/LSF) and AWS (e.g., Batch/HealthOmics), with cost aware scaling.

Why Choose R&D Partners?

As an employee, you have access to a comprehensive benefits package including:

• Medical insurance – PPO, HMO &
• Dental & Vision insurance
• 401k plan
• Employee Assistance Program
• Long-term disability
• Weekly payroll
• Expense reimbursement
• Online timecard approval

Pay Scale:

$135,898 - $169,876 Dependent on Experience)

R&D Partners is a global functional service provider and strategic staffing resource specializing in scientific, clinical research & engineering. We provide job opportunities within major pharmaceutical, biopharmaceutical, biotechnology, and medical device companies.  

R&D Partners is an equal-opportunity employer.