kraken_metagenomics

docker-kraken_metagenomics

Docker image with Kraken software.

Kraken assigns taxonomic labels to short DNA sequences, usually obtained by metagenomic studies

Usage

You can download and run this image using the following commands:

# Get Docker image
docker pull ummidock/kraken_metagenomics:v0.10.6-unreleased

# Analyse the data with minikraken DB
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/kraken_metagenomics:v0.10.6-unreleased kraken --preload --fastq-input --db minikraken_20141208 --threads 2 --output /data/minikraken.sample.txt --paired --gzip-compressed /data/sample_1.fastq.gz /data/sample_2.fastq.gz

# Get Kraken report
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/kraken_metagenomics:v0.10.6-unreleased kraken-report --db minikraken_20141208 /data/minikraken.sample.txt > /local/folder/data/minikraken.sample.report.txt