With increasing scale and complexity of current metagenomic studies approaching terabase-volumes of sequence data, scalability of biological analysis software has become an essential requirement. Toward that end, we have developed JCVI Metagenomics Reports (METAREP), an open-source tool, which integrates the highly scalable search engine Solr/Lucene, R, and CAKEPHP into an extendible Web-based software to query, browse, compare, and share extremely large volumes of metagenomic annotations. The software allows flexible and simultaneous comparison of taxonomic and biological pathway and individual enzyme abundances across hundreds of samples. In this chapter, we provide an overview of this functionality, data format, import, installation, and customization. We present new features that have been released with version 1.4.0 including the implementation of two-way statistical tests to compare features of two datasets without replicates, protein sequence integration, and BLASTP homology...
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abubucker S, Segata N, Goll J, Schubert AM, Izard J, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8:e1002358. doi:10.1371/journal.pcbi.1002358.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. doi:10.1016/S0022-2836(05)80360-2.
Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12:356. doi:10.1186/1471-2105-12-356.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25:25–9. doi:10.1038/75556.
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311:496–503. doi:10.1126/science.1120250.
Goecks J, Nekrutenko A, Taylor J, Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86. doi:10.1186/gb-2010-11-8-r86.
Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, et al. METAREP: JCVI metagenomics reports–an open source tool for high-performance comparative metagenomics. Bioinformatics. 2010;26:2631–2. doi:10.1093/bioinformatics/btq455.
Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, et al. A case study for large-scale human microbiome analysis using JCVI’s Metagenomics Reports (METAREP). PLoS ONE. 2012;7:e29044. doi:10.1371/journal.pone.0029044.
Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371–3.
Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–85. doi:10.1128/MMBR.68.4.669-685.2004.
Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012;486:215–21. doi:10.1038/nature11209.
Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 2004;32:D235–9. doi:10.1093/nar/gkh117.
Markowitz VM, Chen I-MA, Chu K, Szeto E, Palaniappan K, et al. IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project. PLoS ONE. 2012;7:e40151. doi:10.1371/journal.pone.0040151.
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386. doi:10.1186/1471-2105-9-386.
Milligan, Glenn W. An examination of the effect of six types of error perturbation on fifteen clustering algorithms. Psychometrika1980;45(3):325–342.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290–301. doi:10.1093/nar/gkr1065.
Stein LD. The case for cloud computing in genome informatics. Genome Biol. 2010;11:207. doi:10.1186/gb-2010-11-5-207.
Sun S, Chen J, Li W, Altintas I, Lin A, et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 2011;39:D546–51. doi:10.1093/nar/gkq1102.
Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, et al. The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Stand Genomic Sci. 2010;2:229–37. doi:10.4056/sigs.651139.
White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009;5:e1000352. doi:10.1371/journal.pcbi.1000352.
Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008;9:R151. doi:10.1186/gb-2008-9-10-r151.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this entry
Cite this entry
Goll, J. (2015). METAREP, Overview. In: Nelson, K.E. (eds) Encyclopedia of Metagenomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7478-5_238
Download citation
DOI: https://doi.org/10.1007/978-1-4899-7478-5_238
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-7477-8
Online ISBN: 978-1-4899-7478-5
eBook Packages: Biomedical and Life SciencesReference Module Biomedical and Life Sciences