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6.8 General Toolkits
(i) CAMERA: CAMERA provides users with a rich, unique data bank and bioinformatics tools collection for metagenomics reads processing and allows
researchers to disclose the biology of environmental microorganisms. Online
website is for the same is http://camera.calit2.net (Seshadri et al. 2007)
(ii) IMG/M: Integrated Microbial Genomes and Metagenome allows users to do
comparative analysis of a soil microbiome. It is online accessible at http://
img.jgi.doe.gov/m (Markowitz et al. 2012).
(iii) MEGAN: MEGAN is a widely utilized tool for the analysis of metagenomics;
rRNA reads along with the meta-transcriptome and metaproteome datasets
(Huson et al. 2007).
(iv) METAREP: METAREP or JCVI Metagenomics Reports is a web application
for the analysis and comparison of annotated metagenomics reads. METAREP
is highly suitable for performing the complete analysis from diversity structure to the metabolome. The website of METAREP is http://www.jcvi.org/
metarep (Goll et al. 2010)
(v) MG-RAST: MG-RAST is a high-throughput pipeline for high-performance
computing and analysis of metagenomics datasets. The pipeline allows automated functional assignments of metagenomic datasets by comparison with
already deposited protein and nucleotide banks. Evolutionary and functional
attributes can also be identified. MG-RAST is available at http://metagenomics.nmpdr.org or http://metagenomics.anl.gov. MG-RAST is a fast-growing
and constantly updating tool (Meyer et al. 2008; Wilke et al. 2016).
(vi) SmashCommunity: Smash-Community is a self-sufficient annotation tool and
provides a unique platform appropriate for analysing the datasets from Sanger
and 454 sequencer. Source code and manual of SmashCommunity are available at http://www.bork.embl.de/software/smash (Arumugam et al. 2010).
(vii) STAMP: STAMP is a graphical tool package that facilitates mathematical
hypothesis analysis and plots for analysis of phylogenetic along with functional profiles. The Python source code and binaries of STAMP can be downloaded from http://kiwi.cs.dal.ca/Software/STAMP (Parks et al. 2014).
(viii) VAMPS: VAMPS, the “Visualization and Analysis of Microbial Population
Structures,” assists researchers working on projects with large-scale sequencing data. A VAMP permits researchers via marker gene sequence data for
analysis of microbial community diversity and the interconnection among
communities. VAMPS is online accessible from http://vamps.mbl.edu (Huse
et al. 2014).
(ix) EBI-Metagenomics: EBI metagenomics allows researchers to process raw
genomic reads for function-based attributes analysis and phylogenetic characterization without any difficulty and provides an efficient platform and further automatically stores the data in the European Nucleotide Archive with
the associated metadata. EBI metagenomics is online accessible from http://
www.ebi.ac.uk/metagenomics/ (Hunter et al. 2014a, b).
6 Bioinformatics Tools for Soil Microbiome Analysis
6.8 General Toolkits
(i) CAMERA: CAMERA provides users with a rich, unique data bank and bioinformatics tools collection for metagenomics reads processing and allows
researchers to disclose the biology of environmental microorganisms. Online
website is for the same is http://camera.calit2.net (Seshadri et al. 2007)
(ii) IMG/M: Integrated Microbial Genomes and Metagenome allows users to do
comparative analysis of a soil microbiome. It is online accessible at http://
img.jgi.doe.gov/m (Markowitz et al. 2012).
(iii) MEGAN: MEGAN is a widely utilized tool for the analysis of metagenomics;
rRNA reads along with the meta-transcriptome and metaproteome datasets
(Huson et al. 2007).
(iv) METAREP: METAREP or JCVI Metagenomics Reports is a web application
for the analysis and comparison of annotated metagenomics reads. METAREP
is highly suitable for performing the complete analysis from diversity structure to the metabolome. The website of METAREP is http://www.jcvi.org/
metarep (Goll et al. 2010)
(v) MG-RAST: MG-RAST is a high-throughput pipeline for high-performance
computing and analysis of metagenomics datasets. The pipeline allows automated functional assignments of metagenomic datasets by comparison with
already deposited protein and nucleotide banks. Evolutionary and functional
attributes can also be identified. MG-RAST is available at http://metagenomics.nmpdr.org or http://metagenomics.anl.gov. MG-RAST is a fast-growing
and constantly updating tool (Meyer et al. 2008; Wilke et al. 2016).
(vi) SmashCommunity: Smash-Community is a self-sufficient annotation tool and
provides a unique platform appropriate for analysing the datasets from Sanger
and 454 sequencer. Source code and manual of SmashCommunity are available at http://www.bork.embl.de/software/smash (Arumugam et al. 2010).
(vii) STAMP: STAMP is a graphical tool package that facilitates mathematical
hypothesis analysis and plots for analysis of phylogenetic along with functional profiles. The Python source code and binaries of STAMP can be downloaded from http://kiwi.cs.dal.ca/Software/STAMP (Parks et al. 2014).
(viii) VAMPS: VAMPS, the “Visualization and Analysis of Microbial Population
Structures,” assists researchers working on projects with large-scale sequencing data. A VAMP permits researchers via marker gene sequence data for
analysis of microbial community diversity and the interconnection among
communities. VAMPS is online accessible from http://vamps.mbl.edu (Huse
et al. 2014).
(ix) EBI-Metagenomics: EBI metagenomics allows researchers to process raw
genomic reads for function-based attributes analysis and phylogenetic characterization without any difficulty and provides an efficient platform and further automatically stores the data in the European Nucleotide Archive with
the associated metadata. EBI metagenomics is online accessible from http://
www.ebi.ac.uk/metagenomics/ (Hunter et al. 2014a, b).
6 Bioinformatics Tools for Soil Microbiome Analysis