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Ocean Genomics

Ocean genomics applies high-throughput sequencing to seawater, sediment and host-associated samples to map marine microbiomes, viral communities, and eukaryotic plankton. It draws on Tara Oceans, Malaspina, OceanDNA and MGnify resources to study ocean biogeochemistry, climate response and biodiversity at planetary scale.

Tara OceansMGnifyOceanDNAPR2
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Default learning track

4 phases · ~16–22 weeks

A baseline path through this sector with milestones, prerequisites, and concrete projects. Click Personalize this roadmap above to have the AI tailor pace, depth, and resources to your background and goals.

1

Phase 1 — Foundations

3–4 weeks 30–40 hours

Build the conceptual and quantitative base needed to read papers and follow tutorials in the sector.

Prerequisites

  • Comfortable with basic biology / health-science vocabulary
  • Ability to install software and use a terminal

Skills you'll build

Python or R basicsLinux shellGit/GitHubReading scientific literature

Hands-on projects

Reproducible analysis notebook

Walk through a published tutorial in nf-core/mag + MGnify + QIIME2 and reproduce its results on the provided sample data.

Deliverable: GitHub repo with a Jupyter/Quarto notebook, environment.yml, and README

Milestones

  • Set up reproducible Conda/Mamba environment and a public GitHub repo
  • Read and summarize 3 review papers covering the sector landscape
  • Complete an intro statistics or scripting course end-to-end
Citation · training
QIIME2 amplicon tutorials
QIIME2
Why: Exact sector match (Ocean Genomics)
Dataset · dataset
Tara Oceans data portal
Tara Oceans Consortium
Why: Exact sector match (Ocean Genomics)
2

Phase 2 — Core tools & datasets

4–6 weeks 60–80 hours

Learn the standard analytical stack of the sector and the canonical public datasets used by professionals.

Prerequisites

  • Completed Phase 1 reproducible notebook
  • Working Python/R environment

Skills you'll build

nf-core/mag + MGnify + QIIME2Data wranglingQC & exploratory analysisVersion-controlled pipelines

Hands-on projects

Dataset deep-dive on Tara Oceans + MGnify marine + OceanDNA

Pick one study from Tara Oceans + MGnify marine + OceanDNA, reproduce the headline result, and write a short technical note on what you found.

Deliverable: GitHub repo + 3-page PDF write-up

Milestones

  • Run the official nf-core/mag + MGnify + QIIME2 tutorial end-to-end on real data
  • Download and explore one full dataset from Tara Oceans + MGnify marine + OceanDNA
  • Document a clean QC + analysis pipeline that another person could rerun
Citation · course
Coursera · Metagenomics Specialization (UCSD)
Coursera · UCSD
Why: Exact sector match (Ocean Genomics)
Dataset · dataset
MGnify — metagenomics resource (marine projects)
EMBL-EBI
Why: Exact sector match (Ocean Genomics)
3

Phase 3 — Applied projects

6–8 weeks 80–120 hours

Move from tutorials to original analyses on real questions. Start showing your work publicly.

Prerequisites

  • Phase 2 dataset deep-dive complete
  • Comfortable with the sector's primary tooling

Skills you'll build

End-to-end pipeline designStatistical interpretationScientific writingReproducible reports

Hands-on projects

Tara metagenome re-analysis

Re-process a Tara Oceans sample set through nf-core/mag, recover MAGs, and write a short biogeochemistry-flavored brief.

Deliverable: Reproducible repo + MAG quality table + 4-page brief

Milestones

  • Ship one original mini-analysis on a public dataset with clearly stated hypothesis and limitations
  • Engage with the EMBRC and OceanOmics community (post a question, answer one, or share a notebook)
  • Get peer feedback on at least one project and iterate
Citation · course
Python for Everybody
Coursera · Univ. of Michigan
Why: Exact sector match (Ocean Genomics)
Dataset · dataset
OceanDNA — global eDNA reference
Univ. of Tokyo et al.
Why: Exact sector match (Ocean Genomics)
4

Phase 4 — Portfolio & career launch

3–5 weeks 30–50 hours

Package your work, target real roles, and prepare to interview in the sector.

Prerequisites

  • Phase 3 capstone project shipped
  • 2+ public repos under version control

Skills you'll build

Technical CVPortfolio siteInterview prep (case studies + technical questions)Networking

Hands-on projects

Job-ready portfolio package

Curate 2–3 of your strongest sector projects into a portfolio site with clear case-study writeups, plus a 1-page CV tailored to the target role.

Deliverable: Live portfolio URL + PDF CV + cover letter template

Milestones

  • Publish a portfolio site or pinned GitHub README linking to 2–3 projects
  • Tailor CV to 3 real job ads in the sector and submit applications
  • Practice 5 mock technical interviews with sector-specific case studies
Citation · book
R for Data Science (2e)
Hadley Wickham et al.
Why: Exact sector match (Ocean Genomics)
Dataset · dataset
PR2 — Protist Ribosomal Reference database
PR2 Consortium
Why: Exact sector match (Ocean Genomics)

Curated learning resources

Verified, canonical resources from the official providers in this sector. The AI roadmap builder draws from this same library when it personalizes your roadmap.

Courses

Coursera · Metagenomics Specialization (UCSD)
Coursera · UCSD
Python for Everybody
Coursera · Univ. of Michigan
LinkedIn Learning paths
LinkedIn

Trainings

QIIME2 amplicon tutorials
QIIME2
Software Carpentry lessons
The Carpentries
Kaggle Learn
Kaggle

Documentations

Git & GitHub fundamentals
GitHub Docs

Tools

nf-core/mag — metagenome assembly pipeline
nf-core

Datasets

Tara Oceans data portal
Tara Oceans Consortium
MGnify — metagenomics resource (marine projects)
EMBL-EBI
OceanDNA — global eDNA reference
Univ. of Tokyo et al.
PR2 — Protist Ribosomal Reference database
PR2 Consortium
GenomeNet / KEGG ocean modules
Kanehisa Lab
ENA marine metagenomes (study browser)
ENA / EMBL-EBI

Books

R for Data Science (2e)
Hadley Wickham et al.

Communitys

EMBRC — European Marine Biological Resource Centre
EMBRC

Typical career paths

Marine Metagenomicist

Builds metagenomic/MAG pipelines for ocean microbiomes and links them to biogeochemistry.

eDNA Scientist

Designs eDNA assays and bioinformatic pipelines for biodiversity monitoring of marine ecosystems.

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