pegi3s/spades 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)

⁠Using the SPAdes image in Linux

The SPAdes⁠ manual can be found here⁠. This image allows you to use the main SPAdes scripts, namely:

• spades.py (main executable script)
• dipspades.py (main executable script for dipSPAdes)
• metaspades.py (main executable script for metaSPAdes)
• plasmidspades.py (main executable script for plasmidSPAdes)
• rnaspades.py (main executable script for rnaSPAdes)
• truspades.py (main executable script for truSPAdes)

For instance, you can show the help associated to the spades.py main script by running: docker run --rm pegi3s/spades spades.py --help

To run this main script, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/spades spades.py [options] -o /data

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• data to the actual results directory.
• [options] with the input data and other parameters. Refer to the SPAdes manual⁠ to know how this information should be given.

⁠Test data

To test SPAdes you can download these two E. coli FASTQ files from the examples⁠: left⁠ and right⁠

Then, you can run the main script by adapting the following command: docker run --rm -v /your/data/dir:/data pegi3s/spades spades.py --careful --only-assembler --pe1-1 /data/s_6_1.fastq.gz --pe1-2 /data/s_6_2.fastq.gz -o /data/output

Note that /your/data/dir should point to the directory that contains the input files you have downloaded. The output files will be created in the /data/output directory. You can also speed up the execution by adding -t 4 to tell SPAdes to use 4 threads.

Note: the analysis of these files may take a while.

⁠Using the SPAdes image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

To analyze the test data, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/spades spades.py --careful --only-assembler --pe1-1 /data/s_6_1.fastq.gz --pe1-2 /data/s_6_2.fastq.gz -o /data/output