Associate Scientist - Bioinformatics V*

12 month temp to hire contract

Pays up to $80.50 an hour depending on experience

Foster City, CA

ATR International, Inc. cannot sponsor work visas (H-1B, F-1 STEM OPT with I-983, or similar). Candidates must have valid U.S. work authorization.

About the Company

We are a leading organization in the field of bioinformatics, dedicated to advancing genomic research and providing innovative solutions for complex biological challenges. Our mission is to harness the power of data to drive discoveries that improve human health and the environment. We foster a collaborative and inclusive culture that values diversity and encourages creativity.

About the Role

The Associate Scientist - Bioinformatics will play a crucial role in planning and executing assembly approaches for non-model organisms, ensuring high-quality genomic data and contributing to significant research outcomes.

Responsibilities

• 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.
• Productionize workflows (Nextflow/Snakemake/WDL) with containers (Docker/Singularity) across on prem HPC and AWS; produce clear reports, docs, and release packages.

Qualifications

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

Required Skills

• 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.

Preferred Skills

• Deep genome assembly and/or annotation experience in non model organisms (repeat annotation and evidence driven gene annotation is a plus).
• Demonstrated progress toward T2T completeness (telomeres/centromeres/segmental duplications) and chromosome scale scaffolding.
• Evidence of impact (reference releases, preprints/publications, community datasets) is a plus.

Pay range and compensation package

Pays up to $80.50 an hour depending on experience