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Open source code for AlphaFold 2.
Python library to facilitate genome assembly, annotation, and comparative genomics
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
A tool for generating consensus long-read assemblies for bacterial genomes
geNomad: Identification of mobile genetic elements
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Antimicrobial Resistance Identification By Assembly
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
An AI Agent for Fully Automated Multi-omic Analyses
Novelty-inclusive microbial community profiling of shotgun metagenomes
Processing pipeline for pan-genome visulization and exploration
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
Antibiotic resistance prediction in minutes
A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deepARG-LS.
Simulate metagenomic short reads from one or more populations.
Code for detecting genomic island insertions in clades of microbes.