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Temporary Bioinformatics Software Engineer Jobs (NOW HIRING)

ACL Digital

Bioinformatics Engineer

Foster City, CA

$70 - $80/hr

Bioinformatics Engineer -- T2T Genome Assembly (Non model Organisms) Location: Foster City, CA ... solid software engineering practices (Git, testing, documentation). • Workflow + compute ...

BCC-NIH

Program Principal Engineer

Bethesda, MD · Hybrid

... NCBI bioinformatics software and information retrieval systems * Work with a diverse group of ... Programming experience in a Linux environment * Proficiency in C++ * Experience with MS SQL server ...

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 ...

BCC-NIH

Program Principal Engineer

Bethesda, MD · On-site

... NCBI bioinformatics software and information retrieval systems * Work with a diverse group of ... Programming experience in a Linux environment * Proficiency in C++ * Experience with MS SQL server ...

Roberts Recruiting

Software Engineer

Cambridge, MA

Job Purpose We are seeking a software engineer who is passionate about solving data processing ... Experience in bioinformatics and NGS. * Capable of understanding and translating high-level ...

NYULMC

Senior Bioinformatics Programmer

New York, NY · On-site

Sc. plus a minimum of 3 years' experience in Bioinformatics, Computer Science, Programming, Software Development, or related field Previous experience with NGS data and associated bioinformatics ...

The Rockridge Group

Software Engineer II

Emeryville, CA · On-site

$112K - $154K/yr

Software Engineer II RESEARCH AND DEVELOPMENT - BIOINFORMATICS AND SOFTWARE ENGINEERING We are seeking talented, curious, and self-motivated software engineers to help build the most advanced ...

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Temporary Bioinformatics Software Engineer information

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$43K

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How much do temporary bioinformatics software engineer jobs pay per year?

As of Jun 7, 2026, the average yearly pay for temporary bioinformatics software 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 is the difference between Temporary Bioinformatics Software Engineer vs Bioinformatics Data Analyst?

AspectTemporary Bioinformatics Software EngineerBioinformatics Data Analyst
CredentialsBachelor's or Master's in Bioinformatics, Computer Science, or related fieldBachelor's or Master's in Bioinformatics, Biology, or related field
Work EnvironmentProject-based, software development teams, research labsData interpretation, reporting, research teams
Industry UsageBiotech, pharma, research institutionsHealthcare, research, biotech

Temporary Bioinformatics Software Engineers focus on developing and maintaining bioinformatics tools and pipelines, often working in software development environments. Bioinformatics Data Analysts primarily interpret and analyze biological data, providing insights for research or clinical decisions. While both roles require bioinformatics knowledge, their core responsibilities and work settings differ.

What types of projects and collaborations can a Temporary Bioinformatics Software Engineer expect to be involved in?

As a Temporary Bioinformatics Software Engineer, you will typically work on short-term projects such as developing or maintaining data analysis pipelines, optimizing algorithms for genomic data processing, or integrating software tools with laboratory information management systems. Collaboration is frequent with research scientists, data analysts, and other engineers, often through agile project teams or cross-functional meetings. The fast-paced nature of temporary roles means you’ll need to quickly adapt to new codebases, contribute to ongoing research, and communicate technical findings effectively. This can be a great opportunity to build specialized skills, expand your professional network, and gain exposure to the latest advancements in bioinformatics.

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

To thrive as a Temporary Bioinformatics Software Engineer, you need a solid background in computer science, biology, and programming languages such as Python, R, or Java, often with a degree in bioinformatics or a related field. Familiarity with bioinformatics tools, databases (e.g., BLAST, Ensembl), and experience using version control systems like Git are typically required. Strong analytical thinking, adaptability, and effective communication are crucial for collaborating with multidisciplinary teams and handling changing project needs. These skills enable efficient development and maintenance of software solutions that support complex biological data analysis in a fast-paced, project-driven environment.

What does a Temporary Bioinformatics Software Engineer do?

A Temporary Bioinformatics Software Engineer develops and maintains software tools and applications used in biological and genomic research, typically for a specific short-term project or to cover a staffing gap. They collaborate with scientists to analyze data, automate workflows, and ensure the accuracy of computational methods. Their work often involves writing code, managing databases, and troubleshooting technical issues related to the processing of biological data. Temporary roles usually focus on delivering specific features or supporting research within a defined timeframe.
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Temporary Bioinformatics Software Engineer jobs near you
Infographic showing various Temporary Bioinformatics Software Engineer job openings in the United States as of May 2026, with employment types broken down into 1% Locum Tenens, 1% Internship, 88% Full Time, 4% Temporary, and 6% Contract. Highlights an 88% Physical, 3% Hybrid, and 9% Remote job distribution, with an average salary of $131,053 per year, or $63 per hour.
Bioinformatics Engineer

Bioinformatics Engineer

ACL Digital

Foster City, CA

$70 - $80/hr

Other

Posted 4 days ago

Job description

Title: Bioinformatics Engineer — T2T Genome Assembly (Non model Organisms)

Location: Foster City, CA

Duration: 12 months


Description:

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.


This position offers $70-$80/hr on W2

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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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