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comparison README @ 0:3d74b329068b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:49:43 -0400
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1 Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
2
3 The Mothur Tool Suite repository:
4 - Provides Mothur wrappers for the Mothur tools
5 - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system
6
7 Requirements:
8 - Build utilities (make, GCC, gfortran, etc)
9
10 Installing reference data from silva and greengenes:
11 - There is a Galaxy datamanager for available for Mothur
12
13 RDP reference file (modified for mothur):
14 http://www.mothur.org/wiki/RDP_reference_files
15 - 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.
16 http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
17 - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
18 http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
19 - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
20 http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
21 Silva reference:
22 http://www.mothur.org/wiki/Silva_reference_files
23 - Bacterial references (14,956 sequences)
24 http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
25 - Archaeal references (2,297 sequences)
26 http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
27 - Eukaryotic references (1,238 sequences)
28 http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
29 - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
30 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
31 Alignment database rRNA gene sequences:
32 http://www.mothur.org/wiki/Alignment_database
33 - greengenes reference alignment
34 http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
35 - SILVA (Silva reference)
36 http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
37 Secondary structure mapping files:
38 http://www.mothur.org/wiki/Secondary_structure_map
39 http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
40 http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
41 Lane masks:
42 http://www.mothur.org/wiki/Lane_mask
43 greengenes-compatible mask:
44 - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
45 http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
46 - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
47 http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
48 - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
49 http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
50 SILVA-compatible mask:
51 - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
52 http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
53 Lookup Files for sff flow analysis using shhh.flows:
54 http://www.mothur.org/wiki/Alignment_database