A flexible pipeline for complete analysis of bacterial genomes

SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same species) using genome synteny.

Microbiome Analysis Plotting and Visualization

Kolmogorov Arnold Networks

A parallel implementation of gzip for modern multi-processor, multi-core machines.

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Bioinformatics program inStrain

Rapid comparison and dereplication of genomes

A template for creating modular shiny applications that meet academic standards and are reproducible

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

Python package for detection of chimerism and contamination in prokaryotic genomes.

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

Scripts to download genomes from the NCBI FTP servers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Reorients assembled microbial sequences

Metagenomic AnalySis with QUantitative pipEline

Sequential HMM search for rapid protein domain identification

Helper Functions for Interactive Tree Of Life (iTOL)

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

GTDB and RefSeq-RDP DBs parsed for the addSpecies() dada2 function

Chemical metrics for microbial communities

Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.

Network construction, analysis, and comparison for microbial compositional data

{package} Make beautiful Raincloud plots in R!

Mixed Models for Repeated Measures (MMRM) in R.