pegi3s/sratoolkit repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image allows the usage of the SRA Toolkit⁠ suite. Frequently used tools in this suite are:

• fastq-dump: convert SRA data into fastq format.
• fasterq-dump: convert SRA data into fastq format (faster than fastq-dump).
• prefetch: allows command-line downloading of SRA, dbGaP, and ADSP data.
• sam-dump: convert SRA data to sam format.
• sra-pileup: generate pileup statistics on aligned SRA data.
• vdb-config: display and modify VDB configuration information.
• vdb-decrypt: decrypt non-SRA dbGaP data ("phenotype data").

Additional tools included in this suite are:

• abi-dump: convert SRA data into ABI format (csfasta / qual).
• illumina-dump: convert SRA data into Illumina native formats (qseq, etc.).
• sff-dump: convert SRA data to sff format.
• sra-stat: generate statistics about SRA data (quality distribution, etc.).
• vdb-dump: output the native VDB format of SRA data.
• vdb-encrypt: encrypt non-SRA dbGaP data ("phenotype data").
• vdb-validate: validate the integrity of downloaded SRA data.

To obtain the help of an application, you just need to run: docker run --rm pegi3s/sratoolkit <sratoolkit-application-name> --help (e.g. docker run --rm pegi3s/sratoolkit fastq-dump --help)

⁠Using the SRA Toolkit image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/sratoolkit <sratoolkit-application-name> /data/mydata.sra --outdir /data/outdir

In this command, you should replace:

• /your/data/dir to point to the directory that contains the SRA file you want to convert into a FASTQ file.
• <sratoolkit-application-name> to the name of the SRA Toolkit application you want to use.
• mydata.sra to the actual name of your input file.
• outdir to the actual name of your output directory.

For instance, to download data SRR6175516 using the fastq-dump application, you should run: docker run --rm -v /your/data/dir:/data pegi3s/sratoolkit fastq-dump SRR6175516 --outdir /data

Note: Depending on DNS restrictions from your firewall institution, you may obtain an error message:

fastq-dump.3.0.1 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'www.ncbi.nlm.nih.gov:443

In order to solve it, you need to change your DNS Address. Please follow the steps provided here⁠.