Blog¶

Welcome to the MAD4HATTER pipeline blog. Here you'll find updates, release notes, and important announcements about the pipeline.

Posts¶

• Getting Started with Analysing mad4hatter Pipeline Outputs
  A practical walkthrough from pipeline outputs to analysis: QC and filtering, merging across runs, and common downstream work such as drug-resistance summaries, within-host diversity, relatedness, and non-falciparum detection, including pointers to PGEforge, PGEcore, and related tools.

• Version 1.0.0 Release: Major Output Format Changes
  Release notes for v1.0.0 covering parameter updates (including --pools), standardized column names, new and removed outputs, and tips for migrating from v0.2.2.