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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Todd J Treangen12, Sergey Koren123, Daniel D Sommer1, Bo Liu13, Irina Astrovskaya1, Brian Ondov2, Aaron E Darling4, Adam M Phillippy2 and Mihai Pop13*

Author Affiliations

1 Center for Bioinformatics and Computational Biology, 3125 Biomolecular Sciences Bldg #296, University of Maryland, College Park, MD 20742, USA

2 National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA

3 Department of Computer Science, AV Williams Building, University of Maryland, College Park, MD 20742, USA

4 Genome Center, 451 Health Sciences Drive, University of California, Davis, California 95616, USA

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Genome Biology 2013, 14:R2  doi:10.1186/gb-2013-14-1-r2

Published: 15 January 2013


We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: webcite.