:: DESCRIPTION
DUDes is a reference-based taxonomic profiler with a top-down approach to analyze metagenomic NGS samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Piro VC, Lindner MS, Renard BY.
DUDes: a top-down taxonomic profiler for metagenomics.
Bioinformatics. 2016 Aug 1;32(15):2272-80. doi: 10.1093/bioinformatics/btw150. Epub 2016 Mar 24. PMID: 27153591.
:: DESCRIPTION
Omega is a software for assembling and scaffolding Illumina sequencing data of microbial communities.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Omega: an Overlap-graph de novo Assembler for Metagenomics.
Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.
Bioinformatics. 2014 Jun 19. pii: btu395.
:: DESCRIPTION
MTR is a new method for tackling the drawbacks using clustering at Multiple Taxonomic Ranks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, and Elena Marchiori.
MTR: Taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.
Bioinformatics (2011) 27 (2): 196-203.doi: 10.1093/bioinformatics/btq649
:: DESCRIPTION
TANGO is a tool for the optimal taxonomic assignment of ambiguous pyrosequencing reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.
Further steps in TANGO: improved taxonomic assignment in metagenomics.
Alonso-Alemany D1, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.
BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.
Flexible taxonomic assignment of ambiguous sequencing reads.
Clemente JC, Jansson J, Valiente G.
:: DESCRIPTION
MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Liu B, Pop M:
Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.
Lect Notes Comput Sci 2010, 6053: 101-112
:: DESCRIPTION
MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data.
::DEVELOPER
Folker Meyer, Argonne National Laboratory,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The Metagenomics RAST server – A public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer, D. Paarmann, M. D’Souza, R. Olson , E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez , R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards
BMC Bioinformatics 2008, 9:386 ,
:: DESCRIPTION
FastViromeExplorer is a stand-alone pipeline for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tithi SS, Aylward FO, Jensen RV, Zhang L.
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.
PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. PMID: 29340239; PMCID: PMC5768174.
:: DESCRIPTION
MATAM is a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. It has been applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Pericard P, Dufresne Y, Couderc L, Blanquart S, Touzet H.
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.
Bioinformatics. 2018 Feb 15;34(4):585-591. doi: 10.1093/bioinformatics/btx644. PMID: 29040406.
:: DESCRIPTION
NeSSM is a tool to generate Next-Generation Sequencing (NGS) reads with parameters set by users. The goal of NeSSM is to generate metagenome sequencing reads close to the reality.
NeSSMt is a metatranscriptome simulator. Using a composition table and reference transcripts or genomes (with annotation file)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2013 Oct 4;8(10):e75448. doi: 10.1371/journal.pone.0075448. eCollection 2013.
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
Jia B1, Xuan L, Cai K, Hu Z, Ma L, Wei C.
:: DESCRIPTION
TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics
::DEVELOPER
UCF Computational Biology and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
