Setup and languages
Build the local stack, learn Bash/Python/R/SQL, and use a local AI assistant as a tutor.
Start setup Choose languagesPractical bioinformatics, from setup to interpretation
Bioinformatics Field Guide
A technical learning map for bioinformatics: start with setup and languages, then move quickly into real files, workflows, analysis, and research-grade judgment.
Learning map
Pick a route through the field.
This is not only a chronological blog. Use it like a map: enter at your level, explore by domain, or return when the next reviewed guide is published.
Files and public-data practice
Learn the formats that real bioinformatics work keeps returning to.
Read file typesFrom FASTQ to statistical decisions
Connect workflow engines, nf-core/rnaseq, count matrices, QC reports, DESeq2 models, assumptions, and outlier checks.
Read bulk RNA-seq Read Nextflow overview Build an ONT pipelineMore guides are in review
Future topics will appear here only after they are polished, tested, and ready for readers.
Project resourcesFoundation Series
Follow the linear path when you want structure.
Start here if you want a clean sequence. These are the guides currently published and reviewed.
01
Set Up Your Laptop
Conda, Docker, JupyterLab, VS Code, Ollama, BioChatter
02
Pick Your Languages
Bash, Python, R, SQL, notebooks, AI-assisted learning
03
Learn Real File Types
FASTQ, BAM, VCF, GTF, count matrices, metadata
04
Understand Bulk RNA-seq
nf-core/rnaseq, count matrices, DESeq2 designs, outliers, caveats
05
Understand Nextflow And nf-core/rnaseq
workflow engines, local/HPC/AWS execution, cache, parallelization, test profile
06
Build A Custom ONT Pipeline
DSL2 modules, profiles, minimap2, BAM QC, SQANTI3 annotation, nf-core/nanoseq comparison
07
Choose Workflow Tools And Run Nextflow On AWS
Nextflow, Snakemake, WDL, CWL, AWS Batch, S3 work directories, cost-aware test runs
Reusable resources
Run the examples, not just the articles.
Environment
Conda environment file for the starter bioinformatics stack.
environment.ymlDocker
Dockerfile and Compose setup for the JupyterLab workspace.
docker-compose.ymlBioChatter demo
A tiny local BioChatter + Ollama example for explaining observed output.
demo scriptWeek 2 notebooks
Bash, Python, R, and SQL confidence labs with tiny bioinformatics data.
open resourcesWeek 3 file lab
FASTQ, SAM/BAM, VCF, GTF, BED, bedGraph, bigWig, public-file drill, and expected outputs.
open resourcesWeek 4 RNA-seq designs
nf-core samplesheet, DESeq2 design cheat sheet, and runnable design-matrix demo.
open resourcesWeek 5 Nextflow
nf-core/rnaseq test runner, samplesheet template, quick syntax sheet, and output folder map.
open resourcesWeek 6 ONT pipeline
Custom Nextflow DSL2 skeleton with modules, profiles, samplesheet, params, ONT QC, and SQANTI3 handoff.
open resourcesWeek 7 workflow tools
Workflow manager decision matrix, AWS Batch starter config, tiny Nextflow demo, and cloud cost checklist.
open resources