DrjBreakpointFinder

DrjBreakpointFinder is a pipeline adapted from the software Cassis to discover Direct Repeat Junctions (DRJ) of proviral segments and to precisely localize the breakpoint or excision site inside the DRJ sequences.

DrjBreakpointFinder is a Genscale and BIPAA tool, developed by:

• Stéphanie Robin
• Claire Lemaitre

Installation

git clone git@github.com:stephanierobin/DrjBreakpointFinder.git

Requirements

• perl
• R
• bash
• BLAST
• clustalw
• emboss

To activate conda environments :

conda activate myenv

Usage

sh pipeline.sh -r reads.fa -g genome.fa -i input_directory -o output_directory

Example with the small test dataset:

sh pipeline.sh -r test/reads.fasta -g test/genome.fasta -i test -o test/drj

User manual

Input

• reads.fasta : a fasta file containing reads from virus sequencing (circular form of the proviral segments).
• genome.fasta : a fasta file containing the host genome sequence.

Output

An output directory containing :

• Seven subdirectories :
  • blast : Megablast results
  • readLength : table containing the lengths of reads
  • breakpoint : mismatch vectors, for each read-bac triplet
  • drjPairs_alignments : mismatch vectors, for each pair of DRJs
  • drjPairs_all_segments : intermediate results
  • drjPairs_figures : figures summarizing results, for each pair of DRJs
  • drjPairs_merged_segments : intermediate results
• a file drjPairs_confirmed.tab containing the confirmed DRJ pairs coordinates, and the number of reads which allowed identification of these DRJ pairs.

References

If you use DrjBreakpointFinder, please cite:

Legeai F., Santos B.F., Robin S., Bretaudeau A., Dikow R.B., Lemaitre C., Jouan V., Ravallec M., Drezen J-M., Tagu D., Gyapay G., Zhou X., Liu Shanlin, Webb B.A., Brady S.G., and Volkoff A-N. 2019. Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps. Preprint on BioRxiv: https://www.biorxiv.org/content/10.1101/861310v1.

DrjBreakpointFinder is inspired from the software Cassis, in particular for the precise identification of the breakpoint (or excision site) location, for more details on the algorithms, see:

Lemaitre C., Tannier E., Gautier C., Sagot M.-F.. Precise detection of rearrangement breakpoints in mammalian genomes. BMC Bioinformatics, 2008 9(1):286.

Baudet C., Lemaitre C., Dias Z., Gautier C., Tannier E. and Sagot M-F. 2010. Cassis: Detection of genomic rearrangement breakpoints. Bioinformatics, 2010 26(15):1897-1898.

Contact

To contact a developer, request help, or for any feedback on DrjBreakpointFinder, please use the issue form of github: https://github.com/stephanierobin/DrjBreakpointFinder/issues