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comparison edena_ass_wrapper.xml @ 1:cd6cc6d76708 draft

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Simplify passing repeated params to Python script. Add more info to help sections.
author crs4
date Fri, 18 Oct 2013 14:09:11 -0400
parents 60609a9cef3b
children b8c6a38530eb
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0:60609a9cef3b 1:cd6cc6d76708
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65 </tests> 65 </tests>
66 <help> 66 <help>
67 **What it does** 67 **What it does**
68 68
69 The key parameter for this mode is the overlaps size cutoff (option –m). By default it is set to half of the reads length, which is quite conservative. If your sequencing project is well covered (>50-100x) you may try increasing a bit this value. The minCoverage is an important parameter which is automatically determined. You may check this value in the program output and possibly override it. 69 Edena is an overlaps graph based short reads assembler and is suited to Illumina GA reads. An assembly with Edena is a two step process: overlapping and assembling.
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71 In the assembling step, the overlapping file (produced in the previous step) is provided to the program, as well as some assembly parameters. A set of contigs in FASTA format is outputted. The purpose of having a two step process is that the overlapping file is computed only once and can then be used to produce assemblies with different parameters.
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73 The key parameter for this step is the overlaps size cutoff (option –m). By default it is set to half of the reads length, which is quite conservative. If your sequencing project is well covered (>50-100x) you may try increasing a bit this value. The minCoverage is an important parameter which is automatically determined. You may check this value in the program output and possibly override it.
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71 **License and citation** 75 **License and citation**
72 76
73 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 77 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
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