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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Rename contigs 2.0 

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Adds to or replaces contig names.

Quick Start

    • To use Rename contigs 2.0, import your data in fasta format, and a 2-column tab-delimited file where the first column matches the fasta files headers.


Test Data


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

Input File(s)

Use BAt_transcripts_cds.fa and cutWrapper_output.txt 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.

Set the output file name to BA_transcripts_annotated.fasta

Set the type of output to replace

Output File(s)

Expect an output fasta file named BA_transcripts_annotated.fasta.

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