Bioinformatics Engineer

TekWissen•Foster City, CA

1d•Onsite

About The Position

This is a 12-month contract Bioinformatics Engineer role focused on delivering telomere-to-telomere (T2T) reference genomes for non-model organisms. The role involves building and operating long-read assembly and curation pipelines using PacBio HiFi and/or Oxford Nanopore, with complementary data such as Hi-C/Omni-C, Strand-seq, and optical maps. The engineer will collaborate with wet lab and computational teams to address complex genomes (polyploidy, high heterozygosity, repeats) and prepare results for internal and external release.

Requirements

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.
Experience running large genomics workloads on on-prem HPC (e.g., Slurm/LSF) and AWS (e.g., Batch/HealthOmics), with cost-aware scaling.

Nice To Haves

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.
Annotation evidence integration by RNA-Seq and delivery of genome browser enabled tracks.
AWS pipeline operations (S3 data transfer, Batch or HealthOmics).
Strong cross-functional communication (clear status updates, documentation, handoffs).

Responsibilities

Plan assembly approaches for non-model organisms, including data QC, genome profiling, contamination screening, and coverage targets, and advise on sequencing strategy.
Run and iterate long-read assemblies and consensus refinement using tools like hifiasm/Verkko/Flye/Canu, with polishing as appropriate, to achieve chromosome-scale, T2T quality results.
Resolve haplotypes and complex ploidy/heterozygosity using methods such as trio binning and Hi-C/Strand-seq assisted phasing, delivering haplotype-resolved assemblies when required.
Scaffold and curate assemblies with long-range data (e.g., Hi-C/Omni-C, Strand-seq, optical maps), detecting and resolving misjoins, closing gaps where feasible, and documenting curation decisions.
Benchmark quality and completeness using metrics like k-mer spectra/Merqury, BUSCO, QUAST, and read mapping, including repeat, centromere, and telomere assessments to guide iterative improvements.
Productionize workflows using Nextflow/Snakemake/WDL with containers (Docker/Singularity) across on-prem HPC and AWS, producing clear reports, documentation, and release packages.