bracken

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

Unified short-read workflow for multi-marker amplicon (16S, ITS, 18S, gyrB, rpoB, COI) and shotgun taxonomic profiling. Snakemake, conda-based, reproducible.

shotgun metagenomics pipeline to obtain relative abundances and pathway abundances

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

A bioinformatics pipeline for processing and analyzing 16S rRNA amplicon sequencing data using quality control, taxonomic classification, and microbiome profiling workflows.

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

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.

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.

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.

Here we discuss strategies and workflows to analyse metagenomics datasets