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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Index fasta file (Samtools 1.7 faidx)


Creates an index for a fasta file.

Quick Start

Test Data

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

Input File(s)

Use the fasta file, NC_010473.fa from the directory above as test input.

Parameters Used in App

There are no parameters to set for this app.

Output File(s)

Expect a fasta index file named after the input file name. In the test, case, the name is NC_010473.fa.fai

Tool Source for App

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