Job Title: Associate Scientist - Bioinformatics V / Bioinformatics Engineer
Location: Foster City, CA
Duration: 12+ Months
Pay rate: $80/hr on w2
Job Descriptio
nBioinformatics Engineer — T2T Genome Assembly (Non model Organisms
)This is a 12 month contract 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 Responsibiliti
es•Plan assembly approaches for non model organisms (data QC, genome profiling, contamination screening, coverage targets) and advise sequencing strateg
y.•Run and iterate long read assemblies and consensus refinement (e.g., hifiasm/Verkko/Flye/Canu; polishing as appropriate) toward chromosome scale, T2T quality result
s.•Resolve haplotypes and complex ploidy/heterozygosity (e.g., trio binning; Hi C/Strand seq assisted phasing) and deliver haplotype resolved assemblies when require
d.•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 decision
s.•Benchmark quality and completeness (e.g., k mer spectra/Merqury, BUSCO, QUAST, read mapping), including repeat/centromere/telomere assessments to guide iterative improvement
s.•Productionize workflows (Nextflow/Snakemake/WDL) with containers (Docker/Singularity) across on prem HPC and AWS; produce clear reports, docs, and release package
s.
Required Qualificati
ons•PhD in bioinformatics, computational biology, computer science, or related fie
ld.•Proven de novo assembly experience on long reads (PacBio HiFi and/or ONT), including tuning and iterative improveme
nt.•Assembly QC/validation expertise and ability to diagnose common failure modes in complex genom
es.•Strong scripting/programming skills (Python and/or Bash) in Linux; solid software engineering practices (Git, testing, documentatio
n).•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 scali
ng.
Preferred Qualificat
ions•Deep genome assembly and/or annotation experience in non model organisms (repeat annotation and evidence driven gene annotation is a pl
us).•Demonstrated progress toward T2T completeness (telomeres/centromeres/segmental duplications) and chromosome scale scaffold
ing.•Evidence of impact (reference releases, preprints/publications, community datasets) is a p
lus.Additional Skills (Nice to H
ave)•Annotation evidence integration by RNA-Seq and delivery of genome browser enabled tra
cks.•AWS pipeline operations (S3 data transfer, Batch or HealthOmics) and strong cross functional communication (clear status updates, documentation, handof