Contract Metagenomics Jobs (NOW HIRING)

Bioinformatics Engineer - Biosurveillance
As molecular data generation and frontier model intelligence grows, new approaches to data analysis are needed across the biotech industry. Latch is building intelligent, high-performance agents for biological data analysis, empowering over 5,000 scientists across 150+ R&D labs to handle data from instrument-to-insights.
We're seeking a Bioinformatics Engineer to join our Biosurveillance team, working at the frontier of what artificial intelligence can achieve in biology.
About the Role
You will contribute to our technical approach to teaching agents how to understand and handle complex infectious disease surveillance and molecular epidemiology data, working across end-to-end analysis workflows from sequencing outputs to real scientific decisions.
You will work as part of a team of software engineers and biologists building datasets to teach these agents to reason better across:

• Clinical or environmental metagenomics, including sequencing quality control, taxonomic classification, contamination assessment, pathogen discovery, and metagenomic assembly.
• Viral genome reconstruction, annotation, consensus generation, lineage or subtype assignment, and sequencing quality assessment.
• Variant calling, within-host diversity, mixed infections, haplotype reconstruction, recombination, and reassortment.
• Phylogenetics, phylodynamics, viral evolution, genomic epidemiology, transmission analysis, and outbreak reconstruction.
• Wastewater, air, or environmental surveillance, including mixture analysis, abundance estimation, and integration with clinical surveillance.
• Molecular assay design, including qPCR primers and probes, tiled amplicon schemes, inclusivity and exclusivity analysis, and assay-dropout monitoring.
• Host-response analysis using bulk RNA-seq, single-cell RNA-seq, spatial data, immune-receptor sequencing, or other multiomic measurements.
• Antigenic evolution, immune escape, vaccine-strain selection, antiviral resistance, or viral protein analysis.
• Infectious disease modeling, forecasting, population surveillance, and integration of genomic, epidemiological, and clinical data.
• Public-health bioinformatics, reproducible scientific software, data standards, uncertainty assessment, and communication of results to scientific decision-makers.

Experience across every area is not required. We value candidates who have developed depth in one area and can reason carefully across adjacent disciplines.
Requirements

• 3+ years hands-on experience with infectious disease surveillance, metagenomics, or molecular epidemiology data
• Proficiency in Python and/or R

Culture @ Latch
How we work. Genuinely flexible schedules - we just ask that you communicate when you're coming in later than usual. We care most about hard work and output. We're respectfully opinionated, it will always be us against problems, not each other. Optimize for each other's time and bring solutions, not just problems. You'll join a bench suited to your expertise, but we value cross-domain learning and interoperability across teams.
The office & perks. Waterfront office near Oracle Park, 2x free daily meals, unlimited snacks, company outings most months, and team offsites. Plus a vibrant community: cycling, soccer, figure skating, boxing, run clubs, reading clubs, martial arts, music, game nights.
Compensation & Logistics

• 1099 (or W8-BEN) contract, 40 hrs/week, no end date
• Fully performance-based pay: $120K-$180K, uncapped upside. 2x quota = 2x pay.
• 2-4 week paid ramp - full OTE from day one
• Remote (globally), hybrid, or onsite in SF (onsite preferred)
• Work authorization: OPT visa holders only (not STEM Extension)
• Onsite perks: 2x free meals/day, waterfront office (China Basin), monthly parking (based on availability)
• Candidates with all of the above qualifications + proven management skills will be eligible for more senior positions

Interview Process
Timeline: We move fast: 8-12 days from submission to offer.

1. Intro Screen - Techcnial Recruiter
2. Take-Home Project - HackerRank
3. Technical Interview - Member of Technical Staff
4. Culture Interview - C-Suite (If applicable)
5. Offer