Soapdenovo 2.04

Soapdenovo 2.04

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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

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.

Tool Source for App

• http://soap.genomics.org.cn/soapdenovo.html