ClaMS: A Classifier for Metagenomic Sequences

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 alignm...

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Detalles Bibliográficos
Autores principales: Pati, Amrita, Heath, Lenwood S., Kyrpides, Nikos C., Ivanova, Natalia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Michigan State University 2011
Materias:
Research Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235515/
https://www.ncbi.nlm.nih.gov/pubmed/22180827
http://dx.doi.org/10.4056/sigs.2075298
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author Pati, Amrita
Heath, Lenwood S.
Kyrpides, Nikos C.
Ivanova, Natalia
author_facet Pati, Amrita
Heath, Lenwood S.
Kyrpides, Nikos C.
Ivanova, Natalia
author_sort Pati, Amrita
collection PubMed
description 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 minutes on a laptop with a 2.4 GH× Intel Core 2 Duo processor and 2 GB RAM. ClaMS is meant to be a desktop application for biologists and can be run on any machine under any Operating System on which the Java Runtime Environment can be installed.
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spelling pubmed-32355152011-12-16 ClaMS: A Classifier for Metagenomic Sequences Pati, Amrita Heath, Lenwood S. Kyrpides, Nikos C. Ivanova, Natalia Stand Genomic Sci Research Articles 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 minutes on a laptop with a 2.4 GH× Intel Core 2 Duo processor and 2 GB RAM. ClaMS is meant to be a desktop application for biologists and can be run on any machine under any Operating System on which the Java Runtime Environment can be installed. Michigan State University 2011-11-28 /pmc/articles/PMC3235515/ /pubmed/22180827 http://dx.doi.org/10.4056/sigs.2075298 Text en http://creativecommons.org/licenses/by/2.5/ 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.
spellingShingle Research Articles
Pati, Amrita
Heath, Lenwood S.
Kyrpides, Nikos C.
Ivanova, Natalia
ClaMS: A Classifier for Metagenomic Sequences
title ClaMS: A Classifier for Metagenomic Sequences
title_full ClaMS: A Classifier for Metagenomic Sequences
title_fullStr ClaMS: A Classifier for Metagenomic Sequences
title_full_unstemmed ClaMS: A Classifier for Metagenomic Sequences
title_short ClaMS: A Classifier for Metagenomic Sequences
title_sort clams: a classifier for metagenomic sequences
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235515/
https://www.ncbi.nlm.nih.gov/pubmed/22180827
http://dx.doi.org/10.4056/sigs.2075298
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AT heathlenwoods clamsaclassifierformetagenomicsequences
AT kyrpidesnikosc clamsaclassifierformetagenomicsequences
AT ivanovanatalia clamsaclassifierformetagenomicsequences

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