Bioinformatics Engineer

Net2Source

Foster City, CA

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JOB DETAILS

SALARY

$71.94–$80.50 Per Hour

SKILLS

Agile Programming Methodologies, 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, Identify Issues, Industry/Trade Analysis, Leadership, 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

Join a Global Leader in Workforce Solutions – Net2Source Inc.
Who We Are
Net2Source Inc. isn't just another staffing company, we're a powerhouse of innovation, connecting top talent with the right opportunities. Recognized for 300% growth in the past three years, we operate in 34 countries with a global team of 5,500+. Our mission? To bridge the talent gap with precision—Right Talent. Right Time. Right Place. Right Price.

Bioinformatics Engineer — T2T Genome Assembly (Non model Organisms)
Duration-12 month contract
Location- Foster City, California, 94404

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).

Why Work With Us?
We believe in more than just jobs—we build careers. At Net2Source, we champion leadership at all levels, celebrate diverse perspectives, and empower you to make an impact. Think work-life balance, professional growth, and a collaborative culture where your ideas matter.

Our Commitment to Inclusion & Equity
Net2Source is an equal opportunity employer, dedicated to fostering a workplace where diverse talents and perspectives are valued. We make all employment decisions based on merit, ensuring a culture of respect, fairness, and opportunity for all, regardless of age, gender, ethnicity, disability, or other protected characteristics.

Awards & Recognition
• America's Most Honored Businesses (Top 10%)
• Fastest-Growing Staffing Firm by Staffing Industry Analysts
• INC 5000 List for Eight Consecutive Years
• Top 100 by Dallas Business Journal
• Spirit of Alliance Award by Agile1
Ready to Level Up Your Career?

About the Company

Net2Source

Net2Source Inc. is a Global Workforce Management Solutions Company, headquartered in New Brunswick, NJ with its local offices in Texas, California, Florida, Illinois, Colorado and Michigan and its global operations in Canada, UK, Europe, UAE, Malaysia, Australia, China, Singapore and India. Net2Source offers a wide gamut of consulting solutions customized to specific client needs including but not limited to Application Development, Workforce Management and Project Consulting. Whether it’s a Fortune client, whether it’s a System Implementer or whether it is a Start -up, our recipe to success – Exceed expectations! Under promise, over deliver.

COMPANY SIZE

50 to 99 employees

INDUSTRY

Other/Not Classified

WEBSITE

http://www.net2source.com

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