cmonjeau/takeabreak repository overview

⁠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)