ClaMS: A Classifier for Metagenomic Sequences

Amrita Pati, Lenwood S. Heath, Nikos C. Kyrpides, Natalia Ivanova

Abstract


Summary: ClaMS – “Classifier for Metagenomic Sequences” – is a Java application for binning assembled contigs in metagenomes using user-specified training sets and initial parameters. Since ClaMS trains on sequence composition-based genomic signatures, it is much faster than binning tools that rely on alignments to homologs; ClaMS can bin ~20,000 sequences in 3 mins on a Laptop with a 2.4 GHx Intel Core 2 Duo processor and 2 GB RAM. ClaMS is meant to be Desktop application for biologists and can be run on any machine under any Operating System on which Java Runtime Environment can be installed.

Availability: ClaMS is freely available in both GUI-based and command line-based forms and can be obtained from http://clams.jgi-psf.org/.

doi:10.4056/sigs.2075298


Keywords


Metagenome binning, Graph algorithms

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Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.

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