Mercurial > repos > peterjc > fastq_paired_unpaired

diff tools/fastq/fastq_paired_unpaired.xml @ 1:7ed81e36fc1c

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Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
author peterjc
date Mon, 12 Dec 2011 11:33:10 -0500
parents 72e9fcaec61f
children 95a632a71951
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line diff
--- a/tools/fastq/fastq_paired_unpaired.xml	Tue Jun 07 17:21:17 2011 -0400
+++ b/tools/fastq/fastq_paired_unpaired.xml	Mon Dec 12 11:33:10 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.4">
+<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5">
 	<description>using the read name suffices</description>
 	<command interpreter="python">
 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
@@ -52,29 +52,34 @@
 
 Any reads where the forward/reverse naming suffix used is not recognised
 are treated as orphan reads. The tool supports the /1 and /2 convention
-used by Illumina, the .f and .r convention, and the Sanger convention
-(see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details).
+originally used by Illumina, .f and .r convention, the Sanger convention
+(see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
+and the current Illumina convention where the reads get the same identifier
+with the fragment number in the description, for example:
+
+ * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
+ * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA 
 
 Note that this does support multiple forward and reverse reads per template
 (which is quite common with Sanger sequencing), e.g. this which is sorted
 alphabetically:
 
-WTSI_1055_4p17.p1kapIBF
-WTSI_1055_4p17.p1kpIBF
-WTSI_1055_4p17.q1kapIBR
-WTSI_1055_4p17.q1kpIBR
+ * WTSI_1055_4p17.p1kapIBF
+ * WTSI_1055_4p17.p1kpIBF
+ * WTSI_1055_4p17.q1kapIBR
+ * WTSI_1055_4p17.q1kpIBR
 
 or this where the reads already come in pairs:
 
-WTSI_1055_4p17.p1kapIBF
-WTSI_1055_4p17.q1kapIBR
-WTSI_1055_4p17.p1kpIBF
-WTSI_1055_4p17.q1kpIBR
+ * WTSI_1055_4p17.p1kapIBF
+ * WTSI_1055_4p17.q1kapIBR
+ * WTSI_1055_4p17.p1kpIBF
+ * WTSI_1055_4p17.q1kpIBR
 
 both become:
 
-WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
-WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
+ * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
+ * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
 
 	</help>
 </tool>