Bash and Perl scripts associated with research paper "Sister chromatid, but not NHEJ-mediated inter-chromosomal telomere fusions can occur independently of DNA ligases 3 and 4" (Genome Research, 2016).
Scripts rely on the following software.
- BWA (https://sourceforge.net/projects/bio-bwa/files/).
- samtools (https://sourceforge.net/projects/samtools/files/)
- circos (http://circos.ca/software/download/circos/)
- WGP-Toolkit (https://github.com/nestornotabilis/WGP-Toolkit)
To run pipeline:
$ ./run.sh <ID> <PATH TO R1 FASTQ> <PATH TO R2 FASTQ> <PATH TO TELOMERE BWA INDEX> <PATH TO CUSTOM GENOME BWA INDEX> <PATH TO CUSTOM GENOME FASTA>