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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Reference-independent comparative metagenomics using cross-assembly: crAss.

Bas E Dutilh¹, Robert Schmieder, Jim Nulton

¹Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands. dutilh@cmbi.ru.nl

Bioinformatics (Oxford, England)

|October 18, 2012

Summary

This summary is machine-generated.

This study introduces crAss, a bioinformatic tool for analyzing cross-assembly files. It reveals similarities between metagenomic samples, improving comparative metagenomics by utilizing unknown sequences.

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Area of Science:

Bioinformatics
Metagenomics
Computational Biology

Background:

Metagenomes contain many unknown sequences, often ignored in analyses, leading to biased conclusions.
Comparative metagenomics studies relationships between different metagenomic samples.
Cross-assembly links homologous reads from multiple samples without reference databases.

Purpose of the Study:

To introduce a novel bioinformatic tool for analyzing cross-assembly data.
To enable efficient comparative metagenomics by incorporating previously unanalyzed sequences.
To provide insights into metagenomic sample similarities.

Main Methods:

Development of the crAss bioinformatic tool.
Utilizing cross-assembly of reads from multiple metagenomic samples.
Analysis of cross-assembly files to determine sample relationships.

Main Results:

The crAss tool facilitates fast and simple analysis of cross-assembly files.
It generates distances between all pairs of metagenomic samples.
An insightful visualization displays the similarities between samples.

Conclusions:

crAss enhances comparative metagenomics by enabling the analysis of previously ignored unknown sequences.
The tool provides a fast and intuitive method for assessing metagenomic sample relationships.
Cross-assembly analysis with crAss offers a more comprehensive understanding of metagenomic data.