pegi3s/abyss

Sponsored OSS

By i3S

Updated 9 months ago

ABySS (https://github.com/bcgsc/abyss) docker image.

Image
Data Science
Machine Learning & AI

666

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

Since the default k-mer size to run an assembly is 64, we have compiled two additional images with --enable-maxk=128 and --enable-maxk=256. Have a look at the Tags tab of the Docker Hub repository in order to choose the most appropriate one.

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 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.

Docker Pull Command

docker pull pegi3s/abyss