greatfireball/ime_jellyfish

By greatfireball

•Updated over 7 years ago

Docker ime for the Jellyfish kmer counter software

Image

893

Overview Tags

greatfireball/ime_jellyfish repository overview

⁠ime_jellyfish

Docker image for the Jellyfish kmer counting software

⁠Prerequisities

In order to run this container you'll need docker installed.

⁠Usage

The docker image provides the Jellyfish⁠ tool. It will run the jellyfish command as entrypoint. Therefore, running a container is as easy as:

docker run --rm greatfireball/ime_jellyfish --version

Just provide all required parameters via command line. Default working directory is /data. Therefore, input data should be mounted using /data volume.

Running the command to count kmers for a local file reads.fasta in the current folder:

docker run --user $(id -u):$(id -g) --rm -v $PWD:/data greatfireball/ime_jellyfish count -m 21 -s 100M -t 10 -C reads.fasta

Quoting from the Wiki⁠:

"This will count canonical (-C) 21-mers (-m 21), using a hash with 100 million elements (-s 100M) and 10 threads (-t 10) in the sequences in the file reads.fasta. The output is written in the file mer counts.jf by default (change with -o switch)."

⁠Releases

The master branch contains a rolling release. The develop branch is used for further development. Specific tags are used for different Jellyfish releases. Latest release is .