Associate Scientist - Bioinformatics V

Position: Associate Scientist - Bioinformatics V*
Title:
Bioinformatics Engineer T2T Genome Assembly (Non model Organisms)
Duration: 12 month contract
Pay Range: $75/hr - $79.92/hr
Location:
Foster City CA

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 Pac Bio 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
**** assembly experience on long reads (Pac Bio 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/Health Omics), with cost aware scaling.

Preferred Qualifications
"Deep genome assembly and/or annotation experience in non model organisms (repeat annotation and evidence driven gene annotation is a plus).
"Demonstrated progress toward T2T completeness (telomeres/centromeres/segmental duplications) and chromosome scale scaffolding.
"Evidence of impact (reference releases, preprints/publications, community datasets) is a plus.
Additional Skills (Nice to Have)
"Annotation evidence integration by RNA-Seq and delivery of genome browser enabled tracks.
"AWS pipeline operations (S3 data transfer, Batch or Health Omics) and strong cross functional communication (clear status updates, documentation, handoffs).