Public | Automated Build

Last pushed: a year ago
Short Description
TakeABreak - Detect inversion breakpoints directly from raw NGS reads - Colib'read tool
Full Description

TakeABreak description

TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads simulated at 2x40x coverage from human chromosome 22 can be treated in less than two hours, with less than 1GB of memory).

Import the dockerfile

git clone https://github.com/cmonjeau/docker-takeabreak.git

Build the dockerfile

docker build -t cmonjeau/takeabreak .

Print TakeABreak help

docker run -it --rm cmonjeau/takeabreak

Run TakeABreak with data (inside /home/user/discoSNP_data directory)

docker run -it --rm -v /home/user/TakeABreak/files:/data cmonjeau/takeabreak -in '/data/toy_example.fasta,/data/toy_example_reads.fasta,/data/toy_example_with_inv.fasta,/data/toy_example_with_inv_reads.fasta' -out /data/result

Run TAkeABreak with GoDocker (http://www.genouest.org/godocker/)

Create a new job with these parameters:

"Container image" : cmonjeau/takeabreak

"Command" :


#!/bin/bash

# command line example (adapt with your data)
TakeABreak -in $GODOCKER_HOME/data/toy_example.fasta,$GODOCKER_HOME/data/toy_example_reads.fasta -out $GODOCKER_HOME/data/result

"Mount volumes" : home(rw)

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Owner
cmonjeau
Source Repository

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