Associate Scientist - Bioinformatics V

Aptask Global Workforce (AGW) is seeking an Associate Scientist - Bioinformatics V for an Onsite position with a Global Biotechnology Company located in Foster City, CA. This is a 12+ month contract opportunity.

This role is focused on delivering telomere to telomere (T2T) reference genomes for non-model organisms. The successful candidate will build and operate long-read assembly and curation pipelines using PacBio HiFi and/or Oxford Nanopore data. You will partner with wet lab and computational teams to troubleshoot complex genomes and package results for internal and external release.

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

Requirements:

• 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

Desired 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
• Annotation evidence integration by RNA-Seq and delivery of genome browser enabled tracks
• AWS pipeline operations (S3 data transfer, Batch or HealthOmics) and strong cross-functional communication (clear status updates, documentation, handoffs)

Pay range: up to $80.49 per hour

Only candidates available and ready to work directly as Aptask Global Workforce (AGW) employees will be considered for this position.

If you have the described qualifications and are interested in this exciting opportunity, apply today!

Aptask Global Workforce (AGW)
ApTask Global Workforce (AGW) is a certified Minority and Veteran workforce solutions company. AGW delivers operational, clinical, lab and professional talent with a strong focus on healthcare and life sciences. The company supports clients with reliable staffing, program expertise and a commitment to quality, speed and consistent delivery.

Benefits of working with ApTask Global Workforce include:

• Medical
• Dental
• Vision
• Sick Pay (for applicable states/municipalities)

Our team stays close to the process and is here to guide you every step of the way. To learn more, please visit our website

ApTask Global Workforce is an Equal Opportunity Employer. Candidates will receive consideration without regard to their race, color, religion, sex, sexual orientation, gender identity, national origin, disability or status as a protected veteran.