What are the responsibilities and job description for the Bioinformatics Engineer - Genome Assembly position at VARITE INC?
VARITE is looking for qualified Associate Scientist - Bioinformatics V in Foster City, CA.
WHAT THE CLIENT DOES?
An American biopharmaceutical company that focuses on researching and developing antiviral drugs used in the treatment of HIV/AIDS, hepatitis B, hepatitis C, influenza, and COVID-19.
WHAT WE DO?
Established in the Year 2000, VARITE is an award-winning minority business enterprise providing global consulting & staffing services to Fortune 1000 companies and government agencies. With 850 global consultants, VARITE is committed to delivering excellence to its customers by leveraging its global experience and expertise in providing comprehensive scientific, engineering, technical, and non-technical staff augmentation and talent acquisition services.
Job Title: Associate Scientist - Bioinformatics V
Location: Foster City, CA
Contract Duration: 12 months
Pay Rate Range: $70.00 - 80.49/hr. on W2
Work Authorization: USC or GC
HERE’S WHAT YOU’LL DO
Summary:
Bioinformatics Engineer — T2T Genome Assembly (Non model Organisms)
- This is a 12 month contract Bioinformatics Engineer role to deliver telomere to telomere (T2T) reference genomes for non-model organisms by building and operating long read assembly and curation pipelines using PacBio HiFi and/or Oxford Nanopore, with complementary data (Hi C/Omni C, Strand seq, optical maps, short reads) as needed. You will partner with wet lab and computational teams to troubleshoot complex genomes (polyploidy, high heterozygosity, repeats) and package results for internal and external release.
Key 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.
Required Qualifications:
- 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.
- 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).
BENEFITS:
We offer a comprehensive benefits package designed to support the health, well-being, and financial security of our employees and their families. Eligible employees may receive:
- Health Insurance: Medical, dental, and vision coverage
- Retirement Plans: Participation in a company-sponsored retirement savings plan.
- Legal Service Plans: Offering access to attorneys for legal advice and representation.
If this opportunity interests you, please respond by clicking on EasyApply.
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VARITE is committed to creating a diverse environment and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, disability, age, or veteran status.
Salary : $70 - $80