Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page) The Mothur Tool Suite repository: - Provides Mothur wrappers for the Mothur tools - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system Installing Tools via the API: This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead - Install ephemeris: pip install ephemeris -U - Use ephemeris to install tools: shed_install -a -t tools.yaml - (You can find a tools.yaml you can use in this repo as well) Installing reference data from silva and greengenes: - There is a Galaxy datamanager for available for Mothur RDP reference file (modified for mothur): http://www.mothur.org/wiki/RDP_reference_files - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6. http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip Silva reference: http://www.mothur.org/wiki/Silva_reference_files - Bacterial references (14,956 sequences) http://www.mothur.org/w/images/9/98/Silva.bacteria.zip - Archaeal references (2,297 sequences) http://www.mothur.org/w/images/3/3c/Silva.archaea.zip - Eukaryotic references (1,238 sequences) http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip - Silva-based alignment of template file for chimera.slayer (5,181 sequences) http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip Alignment database rRNA gene sequences: http://www.mothur.org/wiki/Alignment_database - greengenes reference alignment http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip - SILVA (Silva reference) http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip Secondary structure mapping files: http://www.mothur.org/wiki/Secondary_structure_map http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip Lane masks: http://www.mothur.org/wiki/Lane_mask greengenes-compatible mask: - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter SILVA-compatible mask: - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter Lookup Files for sff flow analysis using shhh.flows: http://www.mothur.org/wiki/Alignment_database