Mercurial > repos > serranop > usearch
changeset 29:29cb532fc1ee draft
Uploaded
author | serranop |
---|---|
date | Sat, 14 Sep 2013 12:27:32 -0400 |
parents | dcad0a24bafa |
children | 7794d10e6e29 |
files | usearch_fastq_mergepairs.xml |
diffstat | 1 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/usearch_fastq_mergepairs.xml Sat Sep 14 12:20:18 2013 -0400 +++ b/usearch_fastq_mergepairs.xml Sat Sep 14 12:27:32 2013 -0400 @@ -43,7 +43,8 @@ <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<=q, if present. 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" help="'0' means no quality truncation." /> + <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." /> <param name="ascii" type="integer" value="33" label="10. ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" /> @@ -118,7 +119,8 @@ **Manual** -http://drive5.com/usearch/manual/fastq_mergepairs.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**