pegi3s/spades

Sponsored OSS

By i3S

Updated 4 months ago

SPAdes (http://spades.bioinf.spbau.ru) docker image.

Image
Data Science
Machine Learning & AI
1

634

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. For instance, it took 100 minutes to complete using 4 threads on a Ubuntu 14.04.3 LTS with an Intel(R) Core(TM) i5 @ 2.20GHz processor, 16GB of RAM and SSD disk.

Docker Pull Command

docker pull pegi3s/spades