pegi3s/abyss
ABySS (https://github.com/bcgsc/abyss) docker image.
666
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
.
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.
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 pegi3s/abyss