Assess Assembly vs whole genome
Assess Assembly vs whole genome is a basic version of the Plantagora projects tool for evaluating assemblies by comparing them to a reference genome.
Quick Start
- To use Assess Assembly vs whole genome*,* import your assembly in fasta format, and a reference genome in fasta format. The reference genome does not have to be for the same species.
- Resources: http://www.plantagora.org/tools_downloads/assembly_evaluation.html.
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory.
Input File(s)
Use arabtest2 and tair10genome.fas 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.
Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
- Default parameters only, no further configuration needed.
OR
- Use these parameters within the DE app interface:
- parameter name - value/setting
- parameter name - value/setting
Output File(s)
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.