Easily constructs pangenomes and calculates population genomic values for many metagenomic samples, from raw reads, bins or reference genomes.

Code repository accompanying the manuscript, Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function

A metatranscriptomic pipeline optimized for the study of microeukaryotes.

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

StaG Metagenomic Workflow Collaboration

Code used to plot results for article in project "Improving digestibility of silage fibre by use of feruloly esterase producing microorganisms as a silage additive"

NBIS/Elixir course: Tools for Reproducible Research

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Sort Linked Read DNA Into Fragment Specific Clusters

🌈 Interactive analysis of metagenomics data

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Development guidlines for software within NBIS.

Prodigal Gene Prediction Software

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Hirbin repository

Fast genome-wide functional annotation through orthology assignment

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data

Clustering cONtigs with COverage and ComposiTion

Kraken taxonomic sequence classification system