62
Table 6.1 Details of different tools and software employed in soil microbial community analysis
Sample
no.
Name
Weblink
References
Tools for assembly and annotation
1.
Genovo
–
Laserson et al. (2011)
2.
khmer
–
Pell et al. (2012)
3.
Meta-IDBA
http://www.cs.hku.hk/~alse/metaidba
Peng et al. (2011)
4.
MetAMOS
https://github.com/treangen/MetAMOS
Treangen et al. (2013)
5.
MetaVelvet
–
Namiki et al. (2012)
6.
MOCAT
http://www.bork.embl.de/mocat/
Kultima et al. (2012)
7.
SOAPdenovo
–
Li et al. (2010)
8.
MetaORFA
–
Ye and Tang (2009)
9.
FragGeneScan
–
Rho et al. (2010)
10.
MetaGeneAnnotator (MGA)
–
Noguchi et al. (2008)
11.
Orphelia
http://orphelia.gobics.de
Hoff et al. (2009)
12.
SILVA
–
Pruesse et al. (2007)
13.
Greengenes
http://greengenes.lbl.gov
DeSantis et al. (2006)
14.
Ribosomal Database Project (RDP)
http://rdp.cme.msu.edu/
Cole et al. (2009)
Tools for taxonomic profiling
1.
AMPHORA2
http://wolbachia.biology.virginia.edu/WuLab/Software.
html
Wu and Scott (2012)
2.
CARMA3
http://webcarma.cebitec.uni-bielefeld.de
Gerlach and Stoye (2011)
3.
ClaMS
–
Pati et al. (2011)
4.
DiScRIBinATE
–
Ghosh et al. (2010)
5.
INDUS
http://metagenomics.atc.tcs.com/INDUS/
Mohammed et al. (2011)
6.
MARTA
–
Horton et al. (2010)
7.
MetaCluster
–
Wang et al. (2012)
8.
MetaPhlAn
http://huttenhower.sph.harvard.edu/metaphlan/
Segata et al. (2012)
6 Bioinformatics Tools for Soil Microbiome Analysis