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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Samtools_faidx

Samtools faidx command, which is intended to produce a specially formatted index of a fasta formatted file. The index is compact and can be used with the Samtools_view command to create a header for a SAM file without a header.

Quick Start

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > samtools_faidx

Input File(s)

The input file is any fasta formatted file. If you are creating a new header for a Sam file without one, then use the reference sequence fasta file used for the alignment represented by the Sam file. Import from URL to get the data into your Discovery Environment account.

A sample input file, NC_010473.fa, is provided in the example_data directory of the Data Store.

No special Parameters are Used with this App

The only input required is the fasta file described above.

Output File(s)

Expect a specially formatted txt file or tab-delimited file as output. For the example data file, NC_010473.fa, the output file will be NC_010473.fa.fai, also provided in the example_data directory.

Tool Source for App