SRA

Description

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This is the NCBI Short Read Archive Toolkit.

       Release notes:

       SRA Toolkit 2.1.7a includes new features in sam-dump tool and vdb-dump tools.  

       Sam-dump now supports slicing across multiple sequences, and dumping
       cSRA files to fasta and fastq formats. In addition, sam-dump has three
       new parameters:
       -=|--hide-identical              Output '=' if base is identical to reference
       --gzip                           Compress output using gzip
       --bzip2                          Compress output using bzip2

       vdb-dump has two new parameters
       -o|--column_enum_short           enumerates columns in short form
       -b|--boolean                     defines how boolean's are printed (1,T)

       We have combined the functionality of two scripts, config-assistant.perl and reference-assistant.perl
       into a single script, configuration-assistant.perl that helps users download the correct references
       for a given cSRA file and configure the user environment for the SRA Toolkit.

Template:App Location Available versions:

• 2.1.7

Running the application using modules

To use sra with the environment modules system at HPC the following commands are available:

Get module information for sra:

$module spider sra

Load the default application module:

$module load sra

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_SRA_DIR - directory where sra is located.
• HPC_SRA_BIN - location of the executables directory
• HPC_SRA_DOC - location of the documentation directory