diff README.txt @ 0:816cb55b5a2d draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author portiahollyoak
date Thu, 02 Jun 2016 11:34:51 -0400
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+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