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Bioinformatics Software Developer Jobs in California

ACL Digital

Bioinformatics Engineer

Foster City, CA

$80/hr

Associate Scientist - Bioinformatics V / Bioinformatics Engineer Location: Foster City, CA Duration ... solid software engineering practices (Git, testing, documentatio n). • Workflow + compute ...

Plasmidsaurus Inc

Bioinformatics Scientist

San Francisco, CA · On-site

$170K - $190K/yr

Position Overview You'll work on the bioinformatics engine powering that impact, wearing many hats ... Is curious about the intersection of biology, algorithms, and software engineering. * Gets excited ...

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Bioinformatics Software Developer information

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How much do bioinformatics software developer jobs pay per hour?

As of Jun 16, 2026, the average hourly pay for bioinformatics software developer in California is $42.23, according to ZipRecruiter salary data. Most workers in this role earn between $41.97 and $42.45 per hour, depending on experience, location, and employer.

What are some common challenges faced by Bioinformatics Software Developers in their daily work?

Bioinformatics Software Developers often work with large and complex biological datasets, which can present challenges in terms of data integration, processing efficiency, and scalability. Keeping up with rapidly evolving research methodologies and integrating new scientific findings into software solutions can also be demanding. Developers must collaborate closely with biologists, researchers, and other IT professionals to ensure that the tools they build meet scientific needs and are user-friendly. Strong problem-solving skills and adaptability help in overcoming technical and domain-specific obstacles, making this a dynamic and intellectually rewarding career choice.

What is a Bioinformatics Software Developer job?

A Bioinformatics Software Developer designs, implements, and optimizes software tools for analyzing biological data, such as genomic sequences or protein structures. They combine expertise in computer science, bioinformatics, and data science to develop algorithms, databases, and pipelines that support research and clinical applications. These developers often work with researchers to streamline data processing, improve efficiency, and enable new discoveries in the life sciences. Strong programming skills in languages like Python, Java, or R, along with knowledge of bioinformatics frameworks, are essential for this role.

What are the key skills and qualifications needed to thrive in the Bioinformatics Software Developer position, and why are they important?

To thrive as a Bioinformatics Software Developer, you need strong programming skills (especially in Python, R, or Java), a solid foundation in computational biology, and typically a degree in computer science, bioinformatics, or a related field. Familiarity with bioinformatics tools (such as BLAST, Bioconductor, or Galaxy), experience with version control systems like Git, and understanding databases and cloud platforms are commonly required. Collaboration, problem-solving abilities, and strong communication skills help facilitate effective teamwork across interdisciplinary scientific teams. These competencies are vital for developing robust software solutions that address complex biological data challenges encountered in research and healthcare settings.

What are popular job titles related to Bioinformatics Software Developer jobs in California? For Bioinformatics Software Developer jobs in California, the most frequently searched job titles are:
What job categories do people searching Bioinformatics Software Developer jobs in California look for? The top searched job categories for Bioinformatics Software Developer jobs in California are:
Bioinformatics Software Developer jobs near you
Infographic showing various Bioinformatics Software Developer job openings in California as of June 2026, with employment types broken down into 100% Full Time. Highlights an 79% Physical, 3% Hybrid, and 18% Remote job distribution, with an average salary of $87,834 per year, or $42.2 per hour.
Bioinformatics Engineer

Bioinformatics Engineer

ACL Digital

Foster City, CA

$80/hr

Other

Posted 12 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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