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comparison sickle.xml @ 6:c6a790326d1e

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moved from test
author nilesh
date Mon, 15 Jul 2013 12:12:41 -0500
parents 98e35d7ce5c9
children dd2ec1b37e96
comparison
equal deleted inserted replaced
5:4f6349319c0a 6:c6a790326d1e
1 <tool id="sickle" name="Sickle"> 1 <tool id="sickle" name="Sickle">
2 <description>Windowed Adaptive Trimming of FastQ data</description> 2 <description>Windowed Adaptive Trimming of FastQ data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.8">zlib</requirement>
5 <requirement type="package" version="1.21.0">sickle</requirement> 4 <requirement type="package" version="1.21.0">sickle</requirement>
6 </requirements> 5 </requirements>
7 <command> 6 <command>
8 sickle $readtype.single_or_paired --quiet 7 sickle $readtype.single_or_paired --quiet
9 8
82 81
83 <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> 82 <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}">
84 <filter>(readtype['single_or_paired'] == 'pe')</filter> 83 <filter>(readtype['single_or_paired'] == 'pe')</filter>
85 </data> 84 </data>
86 </outputs> 85 </outputs>
87 86 <tests>
87 <param name="single_or_paired" value="pe"/>
88 <param name="input_paired1" value="test.f.fastq"/>
89 <param name="input_paired2" value="test.r.fastq"/>
90 <param name="qual_type" value="illumina"/>
91 <param name="qual_threshold" value="20"/>
92 <param name="length_threshold" value="20"/>
93 <param name="no_five_prime" value="false"/>
94 <param name="discard_n" value="false"/>
95 <output name="output_paired1" value="output.f.fastq"/>
96 <output name="output_paired2" value="output.r.fastq"/>
97 <output name="output_paired_single" value="output.fastq"/>
98 </tests>
99
88 <help> 100 <help>
89 Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses. 101 Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.
90 102
91 Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely. 5'-end trimming can be disabled. 103 Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely. 5'-end trimming can be disabled.
92 104