Contract Genome Analyst Jobs (NOW HIRING)

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.

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