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Contract Bioinformatics Engineer Jobs (NOW HIRING)

ACL Digital

Bioinformatics Engineer

Foster City, CA · On-site

$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 ...

Roche

Sr. Manager, Bioinformatics

Santa Clara, CA · Hybrid

$170K - $316K/yr

You will lead an elite team of bioinformatics scientists and software engineers to create bespoke ... complex contract closures. This position is based on-site in Santa Clara, CA or San Diego, CA ...

Roche

Sr. Manager, Bioinformatics

San Diego, CA · Hybrid

$170K - $316K/yr

You will lead an elite team of bioinformatics scientists and software engineers to create bespoke ... complex contract closures. This position is based on-site in Santa Clara, CA or San Diego, CA ...

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How much do contract bioinformatics engineer jobs pay per year?

As of Jun 26, 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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Contract Bioinformatics Engineer jobs near you
Bioinformatics Engineer

Bioinformatics Engineer

ACL Digital

Foster City, CA • On-site

$80/hr

Other

Posted 22 days ago

Job description

Job Title: Associate Scientist - Bioinformatics V / Bioinformatics Engineer

Location: 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 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 Responsibiliti

es•Plan assembly approaches for non model organisms (data QC, genome profiling, contamination screening, coverage targets) and advise sequencing strateg

y.•Run and iterate long read assemblies and consensus refinement (e.g., hifiasm/Verkko/Flye/Canu; polishing as appropriate) toward chromosome scale, T2T quality result

s.•Resolve haplotypes and complex ploidy/heterozygosity (e.g., trio binning; Hi C/Strand seq assisted phasing) and deliver haplotype resolved assemblies when require

d.•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 decision

s.•Benchmark quality and completeness (e.g., k mer spectra/Merqury, BUSCO, QUAST, read mapping), including repeat/centromere/telomere assessments to guide iterative improvement

s.•Productionize workflows (Nextflow/Snakemake/WDL) with containers (Docker/Singularity) across on prem HPC and AWS; produce clear reports, docs, and release package


s.
Required Qualificati

ons•PhD in bioinformatics, computational biology, computer science, or related fie

ld.•Proven de novo assembly experience on long reads (PacBio HiFi and/or ONT), including tuning and iterative improveme

nt.•Assembly QC/validation expertise and ability to diagnose common failure modes in complex genom

es.•Strong scripting/programming skills (Python and/or Bash) in Linux; solid software engineering practices (Git, testing, documentatio

n).•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 scali


ng.
Preferred Qualificat

ions•Deep genome assembly and/or annotation experience in non model organisms (repeat annotation and evidence driven gene annotation is a pl

us).•Demonstrated progress toward T2T completeness (telomeres/centromeres/segmental duplications) and chromosome scale scaffold

ing.•Evidence of impact (reference releases, preprints/publications, community datasets) is a p

lus.Additional Skills (Nice to H

ave)•Annotation evidence integration by RNA-Seq and delivery of genome browser enabled tra

cks.•AWS pipeline operations (S3 data transfer, Batch or HealthOmics) and strong cross functional communication (clear status updates, documentation, handof


fs).
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About ACL Digital

Sourced by ZipRecruiter

ACL Digital is a global digital technology firm based in San Jose, CA, US, operating within the IT and services industry. The company offers a broad spectrum of services and solutions, including digital transformation, product engineering, industry solutions, and design-led experiences, among others. ACL Digital has its roots established in 1991 with the aim to become a leading-edge innovator in the digital space and has since grown significantly to work with an array of global customers. The company's mission incorporates a commitment to aiding customers to achieve their business goals by adopting and accelerating their digital transformation journeys.

Industry

Technology, communication and media

Company size

1,001 - 5,000 Employees

Headquarters location

San Jose, CA, US

Year founded

1992

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