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

Purpose

These data can be used to test my tool delfies on real data, to get a concrete sense of its inputs/outputs and test that it is properly installed.

Description

Genome

I downloaded the genome of Oscheius onirici, accession: GCA_932521025.

I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint, using `seqkit` v2.8.2, giving the FASTA file in this release.

Sequencing data

I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive:

ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27.

ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4.

ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28.

And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets: "map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data.

After sorting with `samtools`, this gives the BAM files in this release.

Running delfies

I then ran `delfies` version 0.6.0 on each BAM and genome, as:

```shdelfies --threads 16 \    --telo_forward_seq TTAGGC \    --breakpoint_type all \    --min_mapq 20 \    --min_supporting_reads 6 \    \${genome} \${bam} \${odirname}```

The three resulting output directories are in this release, prefixed with `delfies_`.

A single, identical breakpoint is found using all three BAMs (see files '*breakpoint_locations.bed').

Data source

The above raw data were produced and released by the Wellcome Sanger Institute as part of projects PRJEB51305 and PRJEB59023.