Mercurial > repos > portiahollyoak > fastuniq
diff README.txt @ 0:816cb55b5a2d draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author | portiahollyoak |
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date | Thu, 02 Jun 2016 11:34:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Thu Jun 02 11:34:51 2016 -0400 @@ -0,0 +1,69 @@ +Introduction: +========================================================================= +FastUniq as an ultrafast de novo tool for removal of duplicates in paired +short DNA sequence reads in FASTQ format. FastUniq identifies duplicates +by comparing sequences between read pairs and does not require complete +genome sequences as prerequisites. FastUniq is capable of simultaneously +handling reads with different lengths and results in highly efficient +running time. + + +Installation: +========================================================================= + +1). Make sure the gcc compiler installed on your computer (Version 4.0 or + above is recommanded). + +2). Download the latest source code package of FastUniq + (e.g. FastUniq-1.1.tar.gz), and uncompress this package. + +3). Open terminal window, and go to "source" folder of the FastUniq. Open + the "makefile" file, go to the "GCC_OPTION" line which is used to + define the compiler arguments. Your can alter it following the gcc + compiler option's instructions as you needed. + +4). Type "make" + +5). Now, "fastuniq" located in "source" folder is ready to use, you can + move it to any location as you need. + + +Unistall: +========================================================================== + +To uninstall FastUniq, remove the "fastuniq" file located in the "source" +folder, or the "fastuniq" file moved to any location. + + +FastUniq Program parameters: +========================================================================== + +-i : The input file list of paired FSATQ sequence files [FILE IN] + Maximum 1000 pairs + + This parameter is used to specify a list of paired sequence files in + FASTQ format as input, in which two adjacent files with reads in the + same order belong to a pair. + +-t : Output sequence format [q/f/p] + q : FASTQ format into TWO output files + f : FASTA format into TWO output files + p : FASTA format into ONE output file + default = q + + This parameter is used to specify sequence format in output file(s). + FastUniq could output read pairs into two files in either FASTQ [q] + or FASTA [f] format, in which reads in the same order belonging to a + pair. FastUniq could also output read pairs into a single file in + FASTA format [p], in which adjacent reads belonging to a pair. + +-o : The first output file [FILE OUT] + +-p : The second output file [FILE OUT] + Optional. ONLY required when output sequence format(-t) is specify as + [q] or [f]. + +-c : Types of sequence descriptions for output [0/1] + 0 : The raw descriptions + 1 : New serial numbers assigned by FastUniq + default = 0