Stars
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Collecting AMP MIC data from different sources, then running a GAN to output promising sequences
Attentive deep learning model for antimicrobial peptide prediction
Processing pipeline for pan-genome visulization and exploration
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Python script for downloading bacterial genomes from NCBI ftp
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Scripts for finding restriction-modification systems in bacterial genomes.
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
Interactive, web tool for exploring pan-genome of bacterial strains
Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.
snakemake-powered cli to download genomes using NCBI datasets
MiniCPM-o 2.6: A GPT-4o Level MLLM for Vision, Speech and Multimodal Live Streaming on Your Phone
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Convert GTDB taxonomy to NCBI taxdump format
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Short Read Sequence Typing for Bacterial Pathogens