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Related Experiment Video

Updated: Aug 27, 2025

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Metagenome analysis using the Kraken software suite.

Jennifer Lu^1,2, Natalia Rincon^3,4, Derrick E Wood^4,5

¹Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. jennifer.lu717@gmail.com.

Nature Protocols

|September 28, 2022

Summary

This summary is machine-generated.

This study presents a protocol for the Kraken suite, a computational pipeline for analyzing metagenomic data. It enables efficient species quantification and pathogen detection in microbial and clinical samples.

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Last Updated: Aug 27, 2025

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Published on: April 4, 2021

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Metagenomic experiments utilize high-throughput DNA sequencing to identify diverse microbial communities.
Accurate computational analysis of sequencing data is essential for characterizing microbial communities.
Existing analysis methods can be complex and time-consuming.

Purpose of the Study:

To introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for metagenomic data analysis.
To facilitate efficient and reproducible classification, quantification, and visualization of metagenomic datasets.
To provide a user-friendly tool for biologists and clinicians.

Main Methods:

The protocol details the execution of Kraken programs using easy-to-use scripts.
It covers two primary scenarios: species quantification in metagenomic samples and pathogen detection in clinical samples.
The protocol is designed for users familiar with the Unix command-line environment.

Main Results:

The protocol enables accurate classification and quantification of microbial species.
It facilitates the detection of pathogenic agents within clinical samples.
The entire analysis process can be completed within 1-2 hours.

Conclusions:

The Kraken suite protocol offers an efficient and reproducible method for metagenomic data analysis.
It empowers biologists and clinicians to perform complex analyses with greater ease.
This tool aids in understanding microbial ecosystems and identifying potential health threats.