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Internship Bioinformatics Software Engineer Jobs

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 ...

Clerkie

Software Engineer Internship

San Francisco, CA · On-site +1

$80/hr

✨ A note before you apply We're hiring Software Engineering Interns! This is a full-time 12 month internship where you'll work closely with our Engineering, Product, and Design teams to build real ...

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How much do internship bioinformatics software engineer jobs pay per hour?

As of Jun 7, 2026, the average hourly pay for internship bioinformatics software engineer in the United States is $25.42, according to ZipRecruiter salary data. Most workers in this role earn between $20.67 and $28.85 per hour, depending on experience, location, and employer.

What is the difference between Internship Bioinformatics Software Engineer vs Bioinformatics Data Analyst?

AspectInternship Bioinformatics Software Engineer
Required CredentialsEnrolled in or recent graduate of Computer Science, Bioinformatics, or related fields
Work EnvironmentResearch labs, biotech companies, or academic institutions
Employer & Industry UsageUsed in biotech, pharmaceutical, and research organizations for software development
Common Search & ComparisonCompared for entry-level software development roles in bioinformatics

While both roles involve working with biological data, an Internship Bioinformatics Software Engineer focuses on developing software tools and algorithms, often requiring programming skills and software development knowledge. A Bioinformatics Data Analyst primarily analyzes biological data, using statistical and data visualization tools. The internship provides hands-on experience in coding and software creation, whereas a data analyst role emphasizes data interpretation and reporting.

What does an Internship Bioinformatics Software Engineer do?

An Internship Bioinformatics Software Engineer assists in developing and maintaining software tools used to analyze biological data, such as DNA sequences or protein structures. They often work under the supervision of senior engineers and scientists to write code, troubleshoot issues, and implement algorithms for biological research. Interns may also help process large datasets, visualize results, and collaborate with interdisciplinary teams. This role provides hands-on experience in both software development and the application of computational methods to biological problems.

What types of projects do Internship Bioinformatics Software Engineers typically work on, and how do these projects contribute to their professional development?

Internship Bioinformatics Software Engineers often work on projects involving the development and optimization of software tools for analyzing large biological datasets, such as genomic sequences or protein structures. These projects frequently require collaboration with biologists and data scientists, offering valuable exposure to interdisciplinary teamwork. Interns may be tasked with writing code, testing algorithms, or visualizing data, all of which build practical skills in both software engineering and bioinformatics. This hands-on experience not only enhances technical proficiency but also helps interns better understand real-world applications in life sciences, setting a strong foundation for future career growth.

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

To thrive as an Internship Bioinformatics Software Engineer, you need a foundational understanding of programming (often in Python, R, or Java), basic knowledge of molecular biology or genomics, and current pursuit of a degree in bioinformatics, computer science, or a related field. Familiarity with bioinformatics tools (such as BLAST, Bioconductor, or Galaxy), version control systems like Git, and experience analyzing biological datasets are typically expected. Strong problem-solving abilities, attention to detail, and effective communication skills help interns collaborate and learn in multidisciplinary teams. These skills and qualities ensure interns can contribute to meaningful research, adapt quickly to new technologies, and facilitate teamwork in complex scientific environments.
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Internship Bioinformatics Software Engineer jobs near you
Infographic showing various Internship Bioinformatics Software Engineer job openings in the United States as of May 2026, with employment types broken down into 82% Full Time, and 18% Contract. Highlights an 88% Physical, 3% Hybrid, and 9% Remote job distribution, with an average salary of $52,867 per year, or $25.4 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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