Bioinformatics Engineer

TekWissen LLC

Foster City, CA

JOB DETAILS
SALARY
$70–$78
SKILLS
Amazon Simple Storage Service (S3), Amazon Web Services (AWS), Bash Scripting, Benchmarking, Bioinformatics, Biology, Biotech and Pharmaceutical, Communication Skills, Computer Operations, Computer Programming, Computer Science, Cross-Functional, Data Modeling, Data Sets, Diversity, Docker, Documentation, Drug Development, Genomics, Git, HIV/AIDS (Acquired Immune Deficiency Syndrome), Hepatitis B, Hepatitis C, Identify Issues, Linux Operating System, Management of Information Systems/Technology (MIS), Polishing, Publications, Python Programming/Scripting Language, Quality Control, Reporting Skills, Research & Development (R&D), Scaffolding, Scripting (Scripting Languages), Software Engineering, T-2 / DS2, Testing, Web Browsers, Workforce Management
LOCATION
Foster City, CA
POSTED
1 day ago
Overview:

TekWissen is a global workforce management provider headquartered in Ann Arbor, Michigan that offers strategic talent solutions to our clients world-wide. The below job opportunity is with one of our Biotech clients who researches develop and commercializes drugs. The company focuses primarily on antiviral drugs used in the treatment of HIV, hepatitis B, hepatitis C, and influenza, including Harvoni and Sovaldi.

Position: Bioinformatics Engineer
Location: Foster City, CA 94404
Duration: 12 Months
Job Type: Temporary Assignment
Work Type: Onsite
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.
Preferred Qualifications
  • 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.
Additional Skills (Nice to Have)
  • 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).
TekWissen Group is an equal opportunity employer supporting workforce diversity.

About the Company

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TekWissen LLC

WE THE TEKWISSEN PEOPLE

TekWissen offers you a broader portfolio of services, industry-leading solutions, and the meaningful innovations that give you greater flexibility and speed to respond to market dynamics, reduced costs and risk to improve enterprise performance, and increased productivity to enable growth.

To keep pace with global market demands, TekWissen keeps its finger on the pulse of change. Our organized approach to guiding a project from its inception to closure. Managing projects is becoming more and more important as we enter the digital era. To cope with the pace that this transition demands, a method is required to manage projects so they can yield quality work, while incorporating efficient use of time and resources.

Project involves identifying which quality standards are relevant to the project and determining how to satisfy them.

It is important to perform quality planning during the Planning Process and should be done alongside the other project planning processes because changes in the quality will likely require changes in the other planning processes, or the desired product quality may require a detailed risk analysis of an identified problem. It is important to remember that quality should be planned, designed, then built in, not added on after the fact.

Capabilities and accomplishments in one TekWissen business enhance the opportunity for success in the others. Put simply, TekWissen's unique combination of attributes promotes success.



COMPANY SIZE
100 to 499 employees
INDUSTRY
Computer/IT Services
FOUNDED
2009
WEBSITE
http://www.tekwissen.com/