pegi3s/takeabreak repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of TakeABreak⁠, a tool that detects inversion breakpoints directly from NGS (Next Generation Sequencing) reads, without the use of any reference genome and without the "reassembly" of the genomes.

⁠Using the TakeABreak image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/takeabreak bash -c "./TakeABreak -in /data/test_reads.fasta,/data/reference_reads.fasta -out /data/output"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• /test_reads.fasta to the test reads you want to use.
• /reference_reads.fasta to the file containing the reference reads you want to use.
• /data/output to the actual name of your output files (.fasta and .h5).

⁠Note 1

The input reads files can be FASTA, FASTQ or GZIPPED.

To see the TakeABreak help, just run docker run --rm pegi3s/takeabreak TakeABreak -help.

⁠Test data

To test the previous commands, you can use two input FASTA files, containing the test reads and the reference reads, available here⁠.

Then, you should simply run: docker run --rm -v /your/data/dir:/data pegi3s/takeabreak bash -c "./TakeABreak -in /data/toy_example_reads.fasta,/data/toy_example_with_inv_reads.fasta -out /data/output"

⁠Note 2

The previous command generates two files:

• .h5: a Graph file in binary format.
• .fasta: a FASTA file containing the canonical representations of the detected inversion breakpoints.

⁠Note 3

Each inversion corresponds to four entries in the FASTA file:

• The first two correspond to the breakpoint sequences that should be present in one genome (a-u,v-b).
• The last two are the corresponding breakpoint sequences in the other genome (a-revcomp(v),revcomp(u)-b).

⁠Using the TakeABreak image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/takeabreak bash -c "./TakeABreak -in /data/test_reads.fasta,/data/reference_reads.fasta -out /data/output"