Starred repositories
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.
Fast and memory-efficient exact attention
BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
Demonstration of AI review of existing functional annotations
family tree visualization built on top of d3
🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies
Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling
Open source comprehensive 2D content creation tool suite for graphic design, digital art, and interactive real-time motion graphics — featuring node-based procedural editing
A Python toolkit for biomedical data integration and harmonization
A high-performance, lock-free concurrent cuckoo filter implementation in Rust
Infering ancestral synteny with hierarchical orthologous groups
A registry of Knowledge Graphs, their data sources, and the ways they fit together.
Code for 'LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders'
EnzyMM - Enzyme Motif Miner - Geometric matching of catalytic motifs in protein structures.
Demonstration of AI review of existing functional annotations
GraphPart, a data partitioning method for ML on biological sequences
A small gui app for Linux to control the fan speed and monitor temps on a ThinkPad
A beautiful, non-destructive, and GPU-accelerated RAW image editor built with performance in mind.