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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.
Ultra-deep search for novel viruses
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Supporting code for uncultivated gut virus manuscript
Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, …
R package for pre-processing of mass and flow cytometry data
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
A set of R scripts for the analysis of microbial profiles
An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.
A tutorial of the BLUPF90 family programs
Code for de novo discovery of viral families in virome data
Hands-on workflow for learning metagenomics including DNA mapping, binning, QC and annotation. Answers and example code available in the branch 'example' or on the practical webpage:
A tool for identifying active prophage elements through read mapping
Code to accompany "Multitable Methods for Microbiome Data Integration"
A pipeline to go from raw sequencing data to high quality bins and pretty plots.
Convert between measurements and z-scores/percentiles for INTERGROWTH-21st and WHO Child Growth Standards, and classify growth patterns.
The Soil Virome Analysis Pipeline (SOVAP) is designed to process, analyze, and annotate viromics and metagenomics data using cutting-edge tools, providing valuable insights into the virome and micr…