Associate Scientist - Bioinformatics V

LanceSoft Inc

Foster City, CA

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JOB DETAILS

SALARY

$80.50 Per Hour

SKILLS

Amazon Simple Storage Service (S3), Amazon Web Services (AWS), Bash Scripting, Benchmarking, Bioinformatics, Biology, Communication Skills, Computer Operations, Computer Programming, Computer Science, Cross-Functional, Data Modeling, Data Sets, Docker, Documentation, Genomics, Git, Identify Issues, Linux Operating System, Management of Information Systems/Technology (MIS), Polishing, Publications, Python Programming/Scripting Language, Quality Control, Reporting Skills, Scaffolding, Scripting (Scripting Languages), Software Engineering, T-2 / DS2, Testing, Web Browsers

LOCATION

Foster City, CA

POSTED

3 days ago

Title: Bioinformatics Engineer T2T Genome Assembly (Non model Organisms)
Location: Foster City, CA
Contract Duration: 12 Months
Pay Range: $60.00 - $80.50 USD hourly on W2

Job Description:
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 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 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; running large genomics workloads on on prem HPC (e.g., Slurm/LSF) and AWS (e.g., Batch/HealthOmics), 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 HealthOmics) and strong cross functional communication (clear status updates, documentation, handoffs).

About the Company

LanceSoft Inc

We are a $125 Million, NMSDC-certified Minority & Woman owned Workforce Solutions Company headquartered in the DC metro area with presence across US with global presence - Canada, Mexico, India, UK, Malaysia, Indonasia, Hongkong, Singapore, UAE. We are specialized in providing Workforce Solutions, SOW project delivery, Engineering Solutions, Creative Services. We currently support 100+ Fortune companies globally and across multiple industry segments. We are currently supporting several massive programs across industry segment nationally/globally (Intel, Ally, AMD, QUALCOMM, Morgan Stanley, Kraft/ Mondelez, MNP, Amdocs, Dell, SanDisk, Medtronic, Becton Dickinson, GE, Lockheed Martin, UTC, L-3 Communications, Caterpillar, BMW, Mercedes Benz, National Grid, Dominion, Energy Future Holdings, PSEG, 3M, Fidelity, Aetna, Humana, Johnson & Johnson, Pfizer, Merck etc).

All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender, identity, national origin, disability, or protected veteran status.

COMPANY SIZE

2,000 to 2,499 employees

INDUSTRY

Staffing/Employment Agencies

FOUNDED

2000

WEBSITE

http://www.lancesoft.com/

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