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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Assembly Stats (assemblathon)

Assembly Stats (assemblathon) generates a list of statistics to characterize a set of contigs in a fasta file.

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> assembly_stats

Input File(s)

Use BAgenomeRay41.fa 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.

  • Specify the expected size of the genome (let's guess at 130,000,000).

Output File(s)

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


Tool Source for App


  1. Updated documentation 08/12/15.