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Bioinformatics Engineer – T2T Genome Assembly (Non-Model Organisms)

Pyramid, Inc

Foster City, CA

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JOB DETAILS
SALARY
$75–$80 Per Hour
JOB TYPE
Full-time
SKILLS
Amazon Web Services (AWS), Analysis Skills, Artificial Intelligence (AI), Bash Scripting, Best Practices, Bioinformatics, Biology, C Programming Language, Cloud Computing, Computer Programming, Computer Science, Consulting, Data Analysis, Data Quality, Docker, Documentation, Genomics, Git, Healthcare, Identify Issues, Linux Operating System, Performance Tuning/Optimization, Polishing, Programming Methodologies, Python Programming/Scripting Language, Reporting Skills, Resource Utilization, Scaffolding, Scalable System Development, Scripting (Scripting Languages), Short Messaging Service (SMS), Software Engineering, T-2 / DS2, Technical Strategy, Technical Writing, Testing
LOCATION
Foster City, CA
POSTED
11 days ago
Immediate need for a talented Bioinformatics Engineer – T2T Genome Assembly (Non-Model Organisms). This is a 06+months contract opportunity with long-term potential and is located in Foster City, CA(Onsite). Please review the job description below and contact me ASAP if you are interested. Job ID: 26-16942 Pay Range: $75/hr - $80/hour. Traveler benefits as per agency package. (Benefits vary by vendor and assignment.) Key Responsibilities: Genome Assembly & Analysis Design assembly strategies for non-model organisms, including genome profiling, contamination screening, sequencing coverage assessment, and data quality evaluation. Generate and optimize de novo genome assemblies using long-read technologies such as PacBio HiFi and Oxford Nanopore. Utilize assembly tools including Hifiasm, Verkko, Flye, Canu, and related technologies. Perform iterative assembly refinement and polishing to achieve chromosome-scale and T2T-quality assemblies. Resolve complex genomic structures involving heterozygosity, polyploidy, repetitive elements, and structural variation. Assembly Curation & Validation Scaffold and curate assemblies using Hi-C, Omni-C, Strand-seq, optical maps, and other long-range genomic data. Identify and resolve assembly errors, misjoins, and gaps. Conduct assembly quality assessments using BUSCO, Merqury, QUAST, k-mer analyses, and read mapping approaches. Evaluate completeness of telomeric, centromeric, and repetitive genomic regions. Workflow Development & Infrastructure Build reproducible and scalable workflows using Nextflow, Snakemake, or WDL. Containerize pipelines using Docker and/or Singularity. Execute large-scale genomics workloads on HPC clusters and AWS cloud environments. Optimize computational performance, scalability, and cloud resource utilization. Collaboration & Delivery Partner with wet-lab scientists, computational biologists, and project stakeholders. Troubleshoot complex assembly challenges and recommend sequencing or analytical strategies. Prepare technical reports, documentation, and genome release packages for internal and external distribution. Key Requirements and Technology Experience: PhD in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related scientific field. Proven experience performing de novo genome assembly using PacBio HiFi and/or Oxford Nanopore sequencing data. Strong expertise with genome assembly tools such as Hifiasm, Verkko, Flye, Canu, or equivalent platforms. Experience evaluating and troubleshooting genome assemblies using BUSCO, Merqury, QUAST, k-mer analysis, and related methodologies. Strong programming and scripting skills in Python and/or Bash. Experience working in Linux environments. Experience with workflow management systems such as Nextflow, Snakemake, or WDL. Experience operating genomics workloads on HPC environments (Slurm, LSF, etc.) and AWS cloud platforms. Strong understanding of software engineering best practices including Git, testing, reproducibility, and documentation. Deep experience with non-model organism genome assembly projects. Experience achieving chromosome-scale or Telomere-to-Telomere (T2T) assemblies. Expertise in haplotype phasing, trio-binning, and assembly of highly heterozygous or polyploid genomes. Experience using Hi-C, Omni-C, Strand-seq, or optical mapping technologies. Genome annotation and repeat annotation experience. Contributions to published genome references, scientific publications, preprints, or community genomic datasets. Our client is a leading Healthcare Industry, and we are currently interviewing to fill this and other similar contract positions. If you are interested in this position, please apply online for immediate consideration. Pyramid Consulting, Inc. provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws. By applying to our jobs you agree to receive calls, AI-generated calls, text messages, or emails from Pyramid Consulting, Inc. and its affiliates, and contracted partners. Frequency varies for text messages. Message and data rates may apply. Carriers are not liable for delayed or undelivered messages. You can reply STOP to cancel and HELP for help. You can access our privacy policy here. #St

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Pyramid, Inc

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