The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating ge…

Assembly and binning of metagenomes

Interpretative standards for AMR genotypes

A collection of modern/faster/saner alternatives to common unix commands.

A DSL for data-driven computational pipelines

scripts to summarize output from Kraken, the taxonomic sequence classifier

A tool for removing redundant genomes from a set of assemblies

Toolkit for processing sequences in FASTA/Q formats

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

Antimicrobial Resistance Identification By Assembly

Useful bash one-liners for bioinformatics.

Scripts to download genomes from the NCBI FTP servers

Pan-genome wide association studies

SPANDx - Comparative genomics for next-generation haploid sequence data