Stars
A Claude Code plugin that automatically captures everything Claude does during your coding sessions, compresses it with AI (using Claude's agent-sdk), and injects relevant context back into future …
Research code accompanying AlphaGenome
A python library for programmatic usage of EBI InterPro Genome Properties.
The Bioinformatician’s Interactive Lab Notebook (BILN) is a smart, dynamic system for tracking experiments, datasets, and workflows. Designed for bioinformaticians, it ensures reproducibility, stru…
Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
DFAST Quality Control: Taxonomy and completeness check
New repo collection for NVIDIA Cosmos: https://github.com/nvidia-cosmos
Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements.
The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery 🧑🔬
A deep learning package for many-body potential energy representation and molecular dynamics
g1: Using Llama-3.1 70b on Groq to create o1-like reasoning chains
Ray is an AI compute engine. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.
Gzip Decompression and Random Access for Modern Multi-Core Machines
A hybrid assembly and MAG recovery pipeline (and more!)
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Convert GTDB taxonomy to NCBI taxdump format
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.