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

49 Citations (Scopus)
24 Downloads (Pure)


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
Issue number24
Publication statusPublished - Dec 2012
Externally publishedYes

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Dive into the research topics of 'Reference-independent comparative metagenomics using cross-assembly: CrAss'. Together they form a unique fingerprint.

Cite this