Reference-independent comparative metagenomics using cross-assembly: CrAss

Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John L. Mokili

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)

Abstract

Motivation: Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.Results: Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.Availability and implementation: crAss is available as a web server at http://edwards.sdsu. edu/crass/, and the Perl source code can be downloaded to run as a stand-alone command line tool.

Original languageEnglish
Pages (from-to)3225-3231
Number of pages7
JournalBioinformatics
Volume28
Issue number24
DOIs
Publication statusPublished - Dec 2012
Externally publishedYes

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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