Simka is a comparative metagenomics method dedicated to NGS datasets.
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Simka is a comparative metagenomics method dedicated to NGS datasets.
It computes a large collection of distances classically used in ecology to compare communities by approximating species counts by k-mer counts.
https://github.com/GATB/simka/tree/v1.3.2
docker run -it --rm cmonjeau/simka /opt/simka/build/bin/simka
docker run -it --rm cmonjeau/simka /opt/simka/build/bin/simka -in /opt/simka/example/simka_input.txt -out results -out-tmp temp_output
docker run -it --rm cmonjeau/simka python /opt/simka/scripts/create_heatmaps.py results
Create a new job with these parameters:
"Container image" : cmonjeau/simka
"Command" :
#!/bin/bash
# command line example (adapt with your data)
/opt/simka/build/bin/simka -in $GODOCKER_HOME/simka_input.txt -out $GODOCKER_HOME/results -out-tmp temp_output
"Mount volumes" : home(rw)
Content type
Image
Digest
Size
304.6 MB
Last updated
almost 10 years ago
docker pull cmonjeau/simka