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Cube Hub Inc.

Bioinformatics Engineer

Foster City, CA · On-site

Foster City, CA Job Duration: 12 months Bioinformatics Engineer -- T2T Genome Assembly (Non model Organisms) Genome Assembly (PacBio HiFi / ONT) This is a 12 month contract Bioinformatics Engineer ...

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ACL Digital

Bioinformatics Engineer

Foster City, CA

$80/hr

Foster City, CA Duration: 12+ Months Pay rate: $80/hr on w2 Job Descriptio nBioinformatics Engineer -- T2T Genome Assembly (Non model Organisms )This is a 12 month contract Bioinformatics Engineer ...

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How much do contract bioinformatics engineer jobs pay per year?

As of Jun 5, 2026, the average yearly pay for contract bioinformatics engineer in the United States is $131,053.00, according to ZipRecruiter salary data. Most workers in this role earn between $96,000.00 and $157,000.00 per year, depending on experience, location, and employer.

What are Contract Bioinformatics Engineers?

Contract Bioinformatics Engineers are professionals who work on a temporary or project basis to analyze biological data using computational tools. They often collaborate with researchers and institutions in fields like genomics, pharmaceuticals, and biotechnology. Their work involves writing code, processing large datasets, and developing algorithms to interpret complex biological information. By working on a contract basis, they provide specialized expertise for specific projects without being permanent employees.

What are the common challenges faced by Contract Bioinformatics Engineers, and how can they be addressed?

Contract Bioinformatics Engineers often face challenges related to rapidly onboarding to new projects, adapting to diverse data pipelines, and working with teams that may use different workflows or tools. To address these challenges, it's important to maintain strong communication with project leads, quickly familiarize yourself with the organization’s data standards, and leverage your experience with a variety of bioinformatics tools and programming languages. Flexibility and the ability to document your work thoroughly will also help ensure smooth collaboration and successful project delivery.

What are the key skills and qualifications needed to thrive as a Contract Bioinformatics Engineer, and why are they important?

To thrive as a Contract Bioinformatics Engineer, you typically need expertise in computational biology, programming (such as Python or R), and a background in life sciences or related fields. Familiarity with bioinformatics tools, next-generation sequencing (NGS) platforms, version control systems, and data analysis software is commonly required. Strong problem-solving abilities, clear communication, and adaptability are crucial soft skills for collaborating with multidisciplinary teams and meeting project deadlines. These skills ensure efficient data interpretation, accurate results, and successful project delivery in a dynamic, contract-based environment.
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Infographic showing various Contract Bioinformatics Engineer job openings in the United States as of May 2026, with employment types broken down into 34% As Needed, 33% Full Time, and 33% Temporary. Highlights an 80% Physical, 2% Hybrid, and 18% Remote job distribution, with an average salary of $131,053 per year, or $63 per hour.
Bioinformatics Engineer

Bioinformatics Engineer

Cube Hub Inc.

Foster City, CA • On-site

Other

This job post has expired today. Applications are no longer accepted.

Job description

Job Title: Bioinformatics Engineer

Job Location: Foster City, CA

Job Duration: 12 months


Bioinformatics Engineer — T2T Genome Assembly (Non model Organisms)

Genome Assembly (PacBio HiFi / ONT)

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).

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