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changeset 30:7794d10e6e29 draft

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Uploaded
author serranop
date Sat, 14 Sep 2013 12:33:28 -0400
parents 29cb532fc1ee
children 38e5953ca25f
files usearch_fastq_mergepairs.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/usearch_fastq_mergepairs.xml	Sat Sep 14 12:27:32 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 12:33:28 2013 -0400
@@ -42,8 +42,8 @@
         <param name="minovlen" 			type="integer" value="0" label="3. Minimum length of the overlap" help="'0' means no minimum." />
         <param name="minmergelen" 		type="integer" value="0" label="4. Minimum length of the merged read" help="'0' means no minimum." />
         <param name="maxmergelen" 		type="integer" value="0" label="5. Maximum length of the merged read" help="'0' means no maximum." />
-        <param name="maxdiffs" 			type="integer" value="0" label="6. Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" />
-        <param name="truncqual" 		type="integer" value="0" label="7. Truncate the forward and reverse reads at the first Q that is equal or less than this value, if present."
+        <param name="maxdiffs" 			type="integer" value="0" label="6. Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed." />
+        <param name="truncqual" 		type="integer" value="0" label="7. Truncate the forward and reverse reads at the first Q that is equal or less than this value, if present"
 			   help="'0' means no quality truncation. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to set this to 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." />
         <param name="minlen" 			type="integer" value="0" label="8. Minimum length of the forward and reverse read, after truncating per option 7 if applicable" help="'0' means no minimum." />
         <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="9. Allow merge of a pair where the alignment is staggered" help="By default, pairs with staggered alignments are discarded." />
@@ -119,8 +119,8 @@
 
 **Manual**
 
-USEARCH `fastq_mergepairs' command options: http://drive5.com/usearch/manual/fastq_mergepairs.html
-FASTQ format options: http://drive5.com/usearch/manual/fastq_params.html
+* USEARCH fastq_mergepairs command options: http://drive5.com/usearch/manual/fastq_mergepairs.html
+* FASTQ format options: http://drive5.com/usearch/manual/fastq_params.html
 
 **Citation**