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PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture
Workflow for host-linkage to antimicrobial resistance genes using metagenomic 3C/Hi-C data
A scalable high-throughput metabolic and biogeochemical functional trait profiler
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http:https://www.iqtree.org
A resistome profiler for Graphing Resistance Out Of meTagenomes
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
A tool for generating consensus long-read assemblies for bacterial genomes
hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Jos…
⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
Finding prophage regions in bacterial genomes using brute force
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
An Antarctic Tour of the Tidyverse: a tutorial created for R-Ladies Chicago
Disease outbreak reconstruction from epidemiological and genetic data
pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria
Reconstruction of transmission trees using genomic data
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Bayesian inference of ancestral dates on bacterial phylogenetic trees
treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
✂️ ⚡ Rapid haploid variant calling and core genome alignment
An implementation of the Grammar of Graphics in R