Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'

<h2>Purpose</h2> <p><br>These data can be used to test my tool&nbsp;<a href="https://github.com/bricoletc/delfies">delfies </a>on real data, to get a concrete sense of its inputs/outputs and test that it is&nbsp;<br>properly installed.</p> <h2>Description</h2> <h3>Genome</h3> <p>I downloaded the genome of&nbsp;<em>Oscheius onirici</em>, accession: <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_932521025.1">GCA_932521025</a>.</p> <p>I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint,&nbsp;<br>using `seqkit` v2.8.2, giving the FASTA file in this release.</p> <h3>Sequencing data</h3> <p>I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive:</p> <ul> <li>ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27.</li> <li>ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4.</li> <li>ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28.<br><br></li> </ul> <p>And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets:&nbsp;<br>"map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data.</p> <p>After sorting with `samtools`, this gives the BAM files in this release.</p> <h3>Running delfies</h3> <p>I then ran `delfies` version 0.6.0 on each BAM and genome, as:</p> <p>```sh<br>delfies --threads 16 \<br>&nbsp; &nbsp; --telo_forward_seq TTAGGC \<br>&nbsp; &nbsp; --breakpoint_type all \<br>&nbsp; &nbsp; --min_mapq 20 \<br>&nbsp; &nbsp; --min_supporting_reads 6 \<br>&nbsp; &nbsp; \${genome} \${bam} \${odirname}<br>```</p> <p>The three resulting output directories are in this release, prefixed with `delfies_`.</p> <p><strong>A single, identical breakpoint is found using all three BAMs</strong> (see files '*breakpoint_locations.bed').</p> <h3>Data source</h3> <p>The above raw data were produced and released by the Wellcome Sanger Institute as part of projects&nbsp;<br><a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB51305">PRJEB51305</a> and <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB59023">PRJEB59023.</a></p>