Difference between revisions of "SRA"
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Revision as of 02:03, 10 August 2012
Description
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.
Available versions
- 2.1.7
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.