SANGSUM (Statistical Analysis of Next Generation Sequencing Using Matlab) 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. |
Welcome >