SRA

Description

sra website  

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.

Execution Environment and 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

Aspera Connect

To download SRA data you can use the "ascp" utility from the Aspera Connect browser plugin package. We have a copy installed and provided by the sra module. A wrapper script ascp.sh that automatically uses the ssh key is available. For instance:

ascp.sh -QT anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz faa

will download the all.faa.tar.gz archive to the faa directory.

Note: if the download fails to start on the first try with a "Session Stop (Error: Client unable to connect to server (check UDP port and firewall))" error just re-run the command. It's a DNS (host name resolution) problem, which will resolve itself.