pegi3s/abyss 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 facilitates the usage of ABySS⁠, a de novo sequence assembler intended for short paired-end reads and large genomes. All abyss-* commands are available in the path. For instance, you can show the abyss-pe help by running docker run --rm pegi3s/abyss abyss-pe -h.

⁠Available images

The default image supports k-mer lengths up to 192 (the ABySS default). In addition, an image with --enable-maxk=256 is provided for larger k-mer sizes. Have a look at the Tags tab of the Docker Hub repository in order to choose the most appropriate one. Note that the -k.128 variant available for older versions is no longer provided, since the current default (192) already covers it.

Note: increasing --enable-maxk increases the memory requirements of ABySS and you may need to adjust some MPI settings for large k-mer sizes, as described here⁠.

⁠Using the ABySS image in Linux: assemble a small synthetic dataset

To test ABySS, you can download and uncompress the test dataset available here⁠.

Then, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/abyss abyss-pe k=25 B=2G name=test in='/data/test-data/reads1.fastq /data/test-data/reads2.fastq' --directory=/data/results

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• results to point to the directory (under data) where results will be generated. Note that this directory must exist before running the analysis as ABySS won't create it.

⁠Using the ABySS 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/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/abyss abyss-pe k=25 B=2G name=test in='/data/test-data/reads1.fastq /data/test-data/reads2.fastq' --directory=/data/results