Supplemental material for the manuscript "Extreme genome scrambling in cryptic Oikopleura dioica species".

<strong>Supplementary material for Oikopleura scrambled genome study</strong> <em>BreakpointsData.tar.xz contains:</em> Pairwise genome alignment files in GFF format in `inst/extdata/Oidioi_pairwise_v3/`. dN / dS computation results in `inst/extdata/dNdS/`. Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`. OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade, N3 the tunicates and N20 the _Ciona_ clade. `BreakpointsData_3.9.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations. The files needed to build the `BreakpointsData` package. <em><strong>Oidioi_pairwise_v3.tar.gz contains:</strong></em> The pairwise alignment files between genomes, in MAF format. A copy of the Nextflow pipeline used to generate them. <em><strong>oist-assembler.tar.gz contains:</strong></em> A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`. A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`. A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`. <em>Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.</em> <em><strong>Oidioi_genomes.tar.gz contains:</strong></em> For each genome, one file (`&lt;genome&gt;.fa`) containing the whole genome sequence and one directory (`&lt;genome&gt;`) containing each chromosome, scaffold or contig of the genome as a separate file. For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object. <em><strong>OrthoFinderRun.tar.xz contains:</strong></em> A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.