Oxford University Press (OUP), Bioinformatics, 24(28), p. 3225-3231
DOI: 10.1093/bioinformatics/bts613
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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. CONTACT: dutilh@cmbi.ru.nl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.