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

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

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

[data-colorid=at6mr0d6aq]{color:#24292e} html[data-color-mode=dark] [data-colorid=at6mr0d6aq]{color:#d1d6db}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.