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6.3 Tools for Functional Profiling
(i) HUMAnN: HUMAnN predicts the presence or absence along with abundance
of microbial pathways in meta-omics data. HUMAnN offers an accurate and
efficient approach for characterization of metabolic pathways and functional
modules of microbial origin in sequencing reads, allowing the assessment of
community roles in metagenomic studies (Abubucker et al. 2012).
(ii) metaSHARK: metaSHARK, a “metabolic search and reconstruction kit,” is a
database and facilitates users with a completely interactive method to explore
the KEGG metabolic network through a www browser. It can be found online
at http://bioinformatics.leeds.ac.uk/shark/ (Hyland et al. 2006).
(iii) PRMT: Predicted-Relative-Metabolic-Turnover, abbreviated as PRMT, allows
exploration of metabolite-space derived from the metagenome and can be used
as a common tool for the analysis of massive DNA sequences or transcriptome
metadata (Larsen et al. 2011).
(iv) RAMMCAP: RAMMCAP, “Rapid-Analysis of Multiple-Metagenome,” provides a better platform for users to cluster and annotate the metagenome of
interest. It was developed on the basis of an ultra-speed processing, fine statistical package and exclusive graphic user interface (GUI). Tool is accessible
from http://tools.camera.calit2.net/camera/rammcap/ (Li 2009).
6.4 Tools for Underlying Interactome
(i) Spar-CC: A command-based inference program that allows users to perform
various important analyses related to the correlation, bootstraps value, and
p-values to find the microbial intercommunications network. Available from
https://bitbucket.org/yonatanf/sparcc (Friedman and Alm 2012).
(ii) CCREPE: CCREPE can be applied for the prediction of microbiome interactions within and between distinct environments and determine their interrelationships under the complex network (Faust et al. 2012)
6.5 Tools for Statistical Tests
(i) Metastats: Metastats was the foremost statistical approach developed specially
to handle questions in medical research. This tool permits the study of parallel
metagenomic reads from two different populations simultaneously and recognizes those characteristics that statistically differentiate the two populations
(Paulson et al. 2011).
(ii) LefSe: LefSe is an approach for genetic biomarker research through distinct
categorization, via their matching and evaluation-consistent biological
6 Bioinformatics Tools for Soil Microbiome Analysis
6.3 Tools for Functional Profiling
(i) HUMAnN: HUMAnN predicts the presence or absence along with abundance
of microbial pathways in meta-omics data. HUMAnN offers an accurate and
efficient approach for characterization of metabolic pathways and functional
modules of microbial origin in sequencing reads, allowing the assessment of
community roles in metagenomic studies (Abubucker et al. 2012).
(ii) metaSHARK: metaSHARK, a “metabolic search and reconstruction kit,” is a
database and facilitates users with a completely interactive method to explore
the KEGG metabolic network through a www browser. It can be found online
at http://bioinformatics.leeds.ac.uk/shark/ (Hyland et al. 2006).
(iii) PRMT: Predicted-Relative-Metabolic-Turnover, abbreviated as PRMT, allows
exploration of metabolite-space derived from the metagenome and can be used
as a common tool for the analysis of massive DNA sequences or transcriptome
metadata (Larsen et al. 2011).
(iv) RAMMCAP: RAMMCAP, “Rapid-Analysis of Multiple-Metagenome,” provides a better platform for users to cluster and annotate the metagenome of
interest. It was developed on the basis of an ultra-speed processing, fine statistical package and exclusive graphic user interface (GUI). Tool is accessible
from http://tools.camera.calit2.net/camera/rammcap/ (Li 2009).
6.4 Tools for Underlying Interactome
(i) Spar-CC: A command-based inference program that allows users to perform
various important analyses related to the correlation, bootstraps value, and
p-values to find the microbial intercommunications network. Available from
https://bitbucket.org/yonatanf/sparcc (Friedman and Alm 2012).
(ii) CCREPE: CCREPE can be applied for the prediction of microbiome interactions within and between distinct environments and determine their interrelationships under the complex network (Faust et al. 2012)
6.5 Tools for Statistical Tests
(i) Metastats: Metastats was the foremost statistical approach developed specially
to handle questions in medical research. This tool permits the study of parallel
metagenomic reads from two different populations simultaneously and recognizes those characteristics that statistically differentiate the two populations
(Paulson et al. 2011).
(ii) LefSe: LefSe is an approach for genetic biomarker research through distinct
categorization, via their matching and evaluation-consistent biological
6 Bioinformatics Tools for Soil Microbiome Analysis