Assembly Stats (assemblathon)
Assembly Stats (assemblathon) generates a list of statistics to characterize a set of contigs in a fasta file.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> assembly_stats
Use BAgenomeRay41.fa from the directory above as test input.
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.
- Specify the expected size of the genome (let's guess at 130,000,000).
Expect a text file named after the input file input_stats, plus some csv files for graphing or use in spreadsheets. For the test case, the output file you will find in the example_data directory is named BAgenomeRay41.fa_stats