Welcome‎ > ‎

Shared Resources

SANGSUM (Statistical Analysis of Next Generation Sequencing Using Matlab)

You may be using Qiime or mothur to analyse your data, but now you have a third option to access quickly to the routine analysis of 16S rRNA 
genes : SANGSUM.

SANGSUM is a script developed with Matlab that can be used either directly under Matlab or as a standalone application. This script will allow you to process a large fasta file with thousands of sequences to perform the following tasks :
-Uchime chimera check
-phylotype assignation with the RDP classifier
-OTU clustering
-Automatic blast of the representative sequences of each OTU
-Export annotated table of raw and relative abundance of the
-Multivariate analysis (in particular a principal component analysis indicating the bionmial confidence interval for each sample)
-UPGMA phylogenetic tree of the representative sequences of each OTU
-Selection of phylotype using an exact probe and/or the RDP classification

Details are described in the manual : http://www.mediafire.com/?s6cnk554bssmhls

For the Matlab-linked version you need a folder with
         SANSGUM2.zip: http://www.mediafire.com/?wh1lmwt3pzjv4uz (extract the files, start matlab, set the path of the folder and type "SANGSUM" in 
         the command window)
         Mothur(withSilvaSeqs) : http://www.mediafire.com/?83p2z0bp8o48d0z 
         (extract the files MOTHUR20.2 and the silva reference sequences)

For the standalone version you need a folder with
         MCRInstaller : http://www.mediafire.com/?jl5elcaxx0vh2lo (to run once)
         SANGSUM2EXE.zip: http://www.mediafire.com/?b41plpk8f16ak1m (extract the files)
         Mothur(withSilvaSeqs) : http://www.mediafire.com/?83p2z0bp8o48d0z (extract the files MOTHUR20.2 and the silva reference sequences)


Please let me know if you find a bug in this program at olivier.zemb@laposte.net.