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Bioinformatics Engineer

Iconma

Foster City, CA

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JOB DETAILS
SALARY
$75.50–$80.50 Per Hour
SKILLS
Amazon Simple Storage Service (S3), Amazon Web Services (AWS), Bash Scripting, Benchmarking, Bioinformatics, Biology, Communication Skills, Computer Operations, Computer Programming, Computer Science, Cross-Functional, Data Modeling, Data Sets, Docker, Documentation, Genomics, Git, Health Plan, Identify Issues, Linux Operating System, Management of Information Systems/Technology (MIS), Polishing, Publications, Python Programming/Scripting Language, Quality Control, Reporting Skills, Scaffolding, Scripting (Scripting Languages), Software Engineering, T-2 / DS2, Testing, Web Browsers
LOCATION
Foster City, CA
POSTED
1 day ago
Our client, a Biopharmaceutical company, is looking for a Bioinformatics Engineer for their Foster City, CA location.
 
Responsibilities:
  • 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.
  • Partner with wet lab and computational teams to troubleshoot complex genomes (polyploidy, high heterozygosity, repeats) and package results for internal and external release.
  • 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.
  • 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).
 
Why Should You Apply?  

About the Company

I

Iconma

ICONMA is a global information consulting management firm providing Professional Staffing Services and Project-Based Solutions for organizations in a broad range of industries.

  • Corporate Headquarters in Troy, Michigan; 20+ locations worldwide.
  • Certified Woman-Owned Business Enterprise (WBE); certified by Women’s Business Enterprise National Council, National Women Business Owners Corporation (NWBOC); and California Public Utilities Commission (CPUC).
  • Founded in 2000
  • 2000+ Employees

The company was founded on the principle that success is derived from delivering high quality service and resources in the most responsive, flexible, and innovative way. ICONMA invests in people and resources with a single goal: To provide our customers with the highest quality service in the most responsive manner. Through its network of offices, ICONMA provides the resources to help clients maintain their competitive advantage.

COMPANY SIZE
2,000 to 2,499 employees
INDUSTRY
Management Consulting Services
EMPLOYEE BENEFITS
401K, Employee Referral Program, Life Insurance
FOUNDED
2000
WEBSITE
https://www.iconma.com/

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