Mercurial > repos > nml > stringmlst

annotate README.rst @ 1:4e03573653fe draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:34:57 -0400
parents fc0f15ca12e0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
1 stringMLST
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
2
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
3 Fast k-mer based tool for multi locus sequence typing (MLST) stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform-independent fashion with minimum dependencies.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
4
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
5 Reference http://jordan.biology.gatech.edu/page/software/stringmlst/
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
6
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
7 Abstract http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.short?rss=1
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
8
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
9 Application Note http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.full.pdf+html
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
10
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
11 Manual http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
12
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
13 Public repository https://github.com/anujg1991/stringMLST
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
14
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
15
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
16
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
17 License listed below:
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
18
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
19 LICENSE TERMS FOR stringMLST
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
20
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
21 1\. INTENT/PURPOSE:
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
22
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
23 stringMLST is free for academic users and requires permission before any commercial use for any version of this code/algorithm.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
24 If you are a commercial user, please contact king.jordan@biology.gatech.edu for permissions.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
25
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
26 2\. LICENSEE:
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
27
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
28 Any person or organization who receives the software with a copy of this license.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
29
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
30 3\. INTELLECTUAL PROPERTY LICENSED:
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
31
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
32 The rights to use, copy, modify, and compile the software,
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
33 subject to the restrictions described in the present document.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
34
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
35 5\. SCOPE OF THE LICENSE
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
36
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
37 \* NON-COMMERCIAL license for research and evaluation purposes ONLY.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
38
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
39 \* NO right to commercialize the software, or any derivative work,
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
40 without separate agreement with the copyright owners.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
41
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
42 6\. MODIFICATION
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
43
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
44 \* License permits licensee to modify the software for their
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
45 research and evaluation purposes.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
46
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
47 7\. REDISTRIBUTION
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
48
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
49 \* License permits licensee to redistribute verbatim copies
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
50 of the software, accompanied with a copy of this license.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
51
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
52 \* License does not permit licensee to redistribute
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
53 modified versions of the software.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
54
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
55 \* License does not permit licensee to commercialize the software
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
56 or any derivative work of the software.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
57
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
58 8\. FEE/ROYALTY
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
59
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
60 \* Licensee pays no royalty for non-commercial license
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
61
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
62 \* Licensee and any third parties must enter a new agreement
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
63 for any use beyond scope of license.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
64
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
65 9\. NO WARRANTY
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
66
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
67 The software is provided "as is" without warranty of any kind,
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
68 either expressed or implied, including, but not limited to, the implied
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
69 warranties of merchantability and fitness for a particular purpose.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
70 The entire risk as to the quality and performance of
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
71 the program is with the Licensee.
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
72
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
73 10\. NO LIABILITY
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
74
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
75 In no event unless required by applicable law or agreed to in writing
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
76 will any copyright owner be liable to Licensee for damages, including any
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
77 general, special, incidental or consequential damages arising out of the
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
78 use or inability to use the program (including but not limited to loss of
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
79 data or data being rendered inaccurate or losses sustained by Licensee
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
80 or third parties or a failure of the program to operate with other programs),
fc0f15ca12e0 planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
nml
parents:
diff changeset
81 even if such holder has been advised of the possibility of such damages.