Journal
BIOINFORMATICS
Volume 28, Issue 24, Pages 3225-3231Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bts613
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Funding
- NSF Division of Biological Infrastructure grant [0850356]
- Division of Environmental Biology grant [1046413]
- Dutch Science foundation (NWO) Veni grant [016.111.075]
- Direct For Biological Sciences
- Division Of Environmental Biology [1046413] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0850356] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [1330800] Funding Source: National Science Foundation
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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.
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