Mercurial > repos > portiahollyoak > fastuniq
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author | portiahollyoak |
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date | Thu, 02 Jun 2016 11:34:51 -0400 |
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1 Introduction: | |
2 ========================================================================= | |
3 FastUniq as an ultrafast de novo tool for removal of duplicates in paired | |
4 short DNA sequence reads in FASTQ format. FastUniq identifies duplicates | |
5 by comparing sequences between read pairs and does not require complete | |
6 genome sequences as prerequisites. FastUniq is capable of simultaneously | |
7 handling reads with different lengths and results in highly efficient | |
8 running time. | |
9 | |
10 | |
11 Installation: | |
12 ========================================================================= | |
13 | |
14 1). Make sure the gcc compiler installed on your computer (Version 4.0 or | |
15 above is recommanded). | |
16 | |
17 2). Download the latest source code package of FastUniq | |
18 (e.g. FastUniq-1.1.tar.gz), and uncompress this package. | |
19 | |
20 3). Open terminal window, and go to "source" folder of the FastUniq. Open | |
21 the "makefile" file, go to the "GCC_OPTION" line which is used to | |
22 define the compiler arguments. Your can alter it following the gcc | |
23 compiler option's instructions as you needed. | |
24 | |
25 4). Type "make" | |
26 | |
27 5). Now, "fastuniq" located in "source" folder is ready to use, you can | |
28 move it to any location as you need. | |
29 | |
30 | |
31 Unistall: | |
32 ========================================================================== | |
33 | |
34 To uninstall FastUniq, remove the "fastuniq" file located in the "source" | |
35 folder, or the "fastuniq" file moved to any location. | |
36 | |
37 | |
38 FastUniq Program parameters: | |
39 ========================================================================== | |
40 | |
41 -i : The input file list of paired FSATQ sequence files [FILE IN] | |
42 Maximum 1000 pairs | |
43 | |
44 This parameter is used to specify a list of paired sequence files in | |
45 FASTQ format as input, in which two adjacent files with reads in the | |
46 same order belong to a pair. | |
47 | |
48 -t : Output sequence format [q/f/p] | |
49 q : FASTQ format into TWO output files | |
50 f : FASTA format into TWO output files | |
51 p : FASTA format into ONE output file | |
52 default = q | |
53 | |
54 This parameter is used to specify sequence format in output file(s). | |
55 FastUniq could output read pairs into two files in either FASTQ [q] | |
56 or FASTA [f] format, in which reads in the same order belonging to a | |
57 pair. FastUniq could also output read pairs into a single file in | |
58 FASTA format [p], in which adjacent reads belonging to a pair. | |
59 | |
60 -o : The first output file [FILE OUT] | |
61 | |
62 -p : The second output file [FILE OUT] | |
63 Optional. ONLY required when output sequence format(-t) is specify as | |
64 [q] or [f]. | |
65 | |
66 -c : Types of sequence descriptions for output [0/1] | |
67 0 : The raw descriptions | |
68 1 : New serial numbers assigned by FastUniq | |
69 default = 0 |