The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.

Quick Start

Test Data

  • Test data for sspace can be found directly from Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> sspace 

Input File(s)

Use frag_1.fastq and frag_2.fastq as the read files.

Use library.txt as the library file.

Use SoapOutputFrag.contig as the contigs file for extension 

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.

  • Set the output file basename to 'test'
  • Check the box to create .dot file for visualization
  • All other parameters should be left as default

Output File(s)

This analysis will generate the following output files/folders: 

  • bowtieoutput
  • dotfiles
  • intermediate_results
  • pairinfo
  • reads
  • test.final.evidence 
  • test.final.scaffolds.fasta 
  • test.logfile.txt 
  • test.summaryfile.txt

 

Tool Source for App

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