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Bioinformatics Engineer

ICONMA, LLC

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
3 days 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

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ICONMA, LLC

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