Sspace

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

• To use sspace, you need at least one paired-end library, a library file and a contigs FASTA file from a previous assembly
• Resources: https://github.com/nsoranzo/sspace_basic/blob/master/README 

Test Data

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

• https://github.com/nsoranzo/sspace_basic/blob/master/README