A simple nextflow pipeline for running kraken2 and bracken in a docker container

Creates a simple OTU table from Kraken2 report.

A Shiny app for taxonomic abundance visualization

This script filters low abundant reads from Bracken outputs for downstream analyses

shotgun metagenomics pipeline to obtain relative abundances and pathway abundances

CMDB Quant Bio Project:Metagenomic pipeline using Kraken2 and Bracken to analyze gut microbiota differences across young, elderly, and centenarian cohorts.

A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.

Integrated 16S + shotgun metagenomics workflow for kvass fermentation (QIIME2, MetaPhlAn4, Kraken2, HUMAnN3, DRAM2) with reproducible outputs.

Multi-omics characterization of the oral-gut-brain axis in Parkinson's disease using shotgun metagenomics, microbial biomarker discovery, and machine learning.

Here we discuss strategies and workflows to analyse metagenomics datasets

A modular, reproducible, and automated Bash pipeline for bacterial isolate whole-genome sequencing analysis from Illumina paired-end reads, including quality control, taxonomic classification, genome assembly, genome characterization, and coverage estimation.