SRA Toolkit¶

The SRA Toolkit and SDK is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The sratools bundle packages version 3.1.1.

Usage example¶

The following command can be executed in the terminal to load the bundle:

1	`module load sratools`

The SRA Toolkit utilities can be run as shown below:

abi-dump
align-info
cache-mgr
check-corrupt
fasterq-dump
fastq-dump
illumina-dump
kdbmeta
ngs-pileup
prefetch
rcexplain
ref-variation
sam-dump
sff-dump
sra-info
srapath
srapath-orig
sra-pileup
sra-pileup-orig
sra-search
sra-stat
sratools
test-sra
var-expand
vdb-config
vdb-decrypt
vdb-dump
vdb-encrypt
vdb-validate

The sratools_shell command can be used to access a shell in the sratools bundle.

1	`sratools_shell`

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

SRA Toolkit is Public Domain.

Primary citation¶

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za