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Last pushed: a year ago
Short Description
Simka is a comparative metagenomics method dedicated to NGS datasets.
Full Description

Simka v.1.3.2 description

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

Print Simka using docker

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

Run simka using Godocker (http://www.genouest.org/godocker/)

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)

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cmonjeau
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