69
response. It is accessible from http://huttenhower.sph.harvard.edu/lefse/
(Segata et al. 2011).
(iii) ShotgunFunctionalizeR: ShotgunFunctionalizeR is a tool for functional comparative assessment of genetically identified reads. This program includes
methods for import, annotation, and visualization of meta-genomics dataset of
shotgun high-throughput sequencing. It is available at http://shotgun.zool.gu.
se
(iv) SourceTracker: SourceTracker is a Bayesian method for estimation of the fraction of a novel community from a group of source environments. It is able to
find the rate of invasion or growth of one community among others in any
particular set of microbiomes (Knights et al. 2011).
6.6 Simulators Tools
(i) GemSIM: General-Error-Model based SIMulators are high-throughput sequencing simulation predictors with the ability of producing the single or paired-end
contigs for any sequencing technology compatible with the generic formats
SAM and FASTQ (McElroy et al. 2012).
(ii) MetaSim: MetaSim is a gene sequence simulation model and can be applied to
create groups of synthetic reads that reveal the phylogenetic relationship of the
usual metagenome (Richter et al. 2008).
6.7 Tools for Single-Cell Sequencing Analysis
(i) IDBA-UD: IDBA-UD is a tool for the assembly of the poor coverage data of the
single-cell or metagenome reads with unequal depths. This tool is based on the
de Bruijn graph and can be found on http://www.cs.hku.hk/~alse/idba_ud (Peng
et al. 2012).
(ii) SmashCell: SmashCell is a automated software framework planned to perform
the microbial genomic processing, that is, assembly, gene prediction, and functional characterization in a manner that facilitates parameter and algorithm
assessment at every step in the process. The source code and manual of
SmashCell are available at http://asiago.stanford.edu/SmashCell (Harrington
et al. 2010)
6.7 Tools for Single-Cell Sequencing Analysis
response. It is accessible from http://huttenhower.sph.harvard.edu/lefse/
(Segata et al. 2011).
(iii) ShotgunFunctionalizeR: ShotgunFunctionalizeR is a tool for functional comparative assessment of genetically identified reads. This program includes
methods for import, annotation, and visualization of meta-genomics dataset of
shotgun high-throughput sequencing. It is available at http://shotgun.zool.gu.
se
(iv) SourceTracker: SourceTracker is a Bayesian method for estimation of the fraction of a novel community from a group of source environments. It is able to
find the rate of invasion or growth of one community among others in any
particular set of microbiomes (Knights et al. 2011).
6.6 Simulators Tools
(i) GemSIM: General-Error-Model based SIMulators are high-throughput sequencing simulation predictors with the ability of producing the single or paired-end
contigs for any sequencing technology compatible with the generic formats
SAM and FASTQ (McElroy et al. 2012).
(ii) MetaSim: MetaSim is a gene sequence simulation model and can be applied to
create groups of synthetic reads that reveal the phylogenetic relationship of the
usual metagenome (Richter et al. 2008).
6.7 Tools for Single-Cell Sequencing Analysis
(i) IDBA-UD: IDBA-UD is a tool for the assembly of the poor coverage data of the
single-cell or metagenome reads with unequal depths. This tool is based on the
de Bruijn graph and can be found on http://www.cs.hku.hk/~alse/idba_ud (Peng
et al. 2012).
(ii) SmashCell: SmashCell is a automated software framework planned to perform
the microbial genomic processing, that is, assembly, gene prediction, and functional characterization in a manner that facilitates parameter and algorithm
assessment at every step in the process. The source code and manual of
SmashCell are available at http://asiago.stanford.edu/SmashCell (Harrington
et al. 2010)
6.7 Tools for Single-Cell Sequencing Analysis