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Notes on bioinformatics, genomics, and computation written for the version of me who was starting out.

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— 2026 —

  1. Creating nf-core-style Nextflow modules

    Nextflow

    A practical guide to writing local Nextflow modules with modern nf-core-style metadata, topic-channel version outputs, stub tests, and nf-test snapshots.

  2. Checking bioinformatics files before you trust them

    Bioinformatics

    A reference for the command-line checks you run before trusting a file, launching a pipeline, or debugging a result.

— 2019 —

  1. Python for Biological Data Analysis, Part 2: Working with Files

    Python

    How to read, write, and append biological sequence files in Python using safe file I/O patterns.

  2. Python for Biological Data Analysis, Part 1: Strings and Sequence Basics

    Python

    A practical introduction to Python string operations for biological sequence analysis.

  3. Extracting Mapped and Unmapped Reads from FASTQ

    Bioinformatics

    A practical command-line workflow to separate mapped and unmapped reads and recover them into FASTQ files.

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