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.
- To use Samtools_faidx, make sure your fasta reference file is entered into the Discovery Environment.
- Resources: http://samtools.sourceforge.net/samtools.shtml#1
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
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.
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.