Soapdenovo 2.04
Soapdenovo 2.04
Community rating: ?????
This is version 2.04 of the Soapdenovo genome assembler
Soapdenovo 2.04
Community rating: ?????
This is version 2.04 of the Soapdenovo genome assembler
Quick Start
To use Soapdenovo 2.04, import your data in fastq format.
Resources: http://soap.genomics.org.cn/soapdenovo.html
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under CommunityData>iplantcollaborative>example_data>Soapdenovo-2.
Input File(s)
Use frag_1.fastq and frag_2.fastq from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below. Leave other parameters as defaults.
Use these parameters within the DE app interface:
maximum read length - 100
average insert size, library 1 - 180
assembly steps, library 1 - assembly and scaffolding
sequence file format, library 1 - q
read orientation, library 1 - Forward,Reverse
kmer size - 39
Output File(s)
Expect a series of files starting with the output prefix as output. For the test case, the output files you will find in the example_data directory is named SoapOutputFrag.scafSeq, SoapOutputFrag.contig.