containerised CLI academic publishing toolkit using Pandoc/LaTeX to build PDFs from Markdown manuscripts

BullshitBench measures whether AI models challenge nonsensical prompts instead of confidently answering them, created by Peter Gostev.

RAIN - RNA Alterations Investigation using Nextflow with particular focus on A-to-I editing events

BRAKER re-implemented with snakemake

Build knowledge graphs from KEGG pathways and see pathway overlap between species

Variant consequence prediction and HGVS notation, concordant with Ensembl VEP.

A tutorial on how to annotate and interpret novel mammalian reference genomes

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.

NanoSpeech: a custom modification-aware basecaller

NanoListener: a small suite of Python scripts to create custom training datasets for modification-aware basecaller models.

A curated list of TUI apps and libraries built with Ratatui

CI workflow to automatically publish selected RSS feeds to a Bluesky account (use case: https://bsky.app/profile/bioinfoblogs.bsky.social)

Containerize your Pixi workspace with a single command!

A planet-like static website to track bioinformatics blogs around the world

A tool to synchronize posts from Bluesky to Mastodon

A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all from the terminal.

k-mer-based non-Bayesian Taxonomic Classifier

Parser of eggnog ANnotated files using KEGG entries (used in RVanDamme/MAFIN)

Monorepo for Apollo 3 server-side and client-side (JBrowse 2 plugin) components.

Foreign Contamination Screening caller scripts and documentation

Pathoscope: Species identification and strain attribution with unassembled sequencing data

A collection of notebooks/recipes showcasing some fun and effective ways of using Claude.

A comprehensive prokaryotic genome annotation pipeline

PMosquito – Assembly of interrupted trajectory data by videotracking

ViroSeek: a viral detection pipeline for second-generation sequencing

Instructions for all major step in a plant genome sequencing project