StrOccCau_1.0_nuc_finalMito_RepeatMasked.fa.bz2 : This file is homology-based and de novo model-based repeat-masking of the reference Strix occidentalis caurina genome StrOccCau_1.0_nuc.fa from Hanna et al., 2017a,b) with the mitochondrial genome from Hanna et al. (2017c). StrOccCau_1.0_nuc_finalMito_RepeatMasked.bed.bgz : This is a file in Browser Extensible Data (BED) format that provides the genomic intervals of the N-regions in the above masked assembly. The N-regions include hard-masked low complexity and repeat regions as well as N-regions that were gaps in the original assembly. I compressed the file using the bgzip tool from HTSlib version 1.7 (Davies et al. 2018). See full details of the creation of these files in section 2.1 of the materials and methods at protocols.io (http://dx.doi.org/10.17504/protocols.io.rmrd456). If you use these data, please cite the following: Hanna ZR. 2018. Repeat-masked Strix occidentalis caurina nuclear genome version 1.0 and complete mitochondrial genome. Version 1.0.0. Zenodo. References Davies R, Randall JC, McCarthy SA, Bonfield J, Pollard MO, Marshall J, et al. 2018. HTSlib. Version 1.7. [Accessed 2018 Mar 19]. Available from: https://github.com/samtools/htslib Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017a. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biology and Evolution. 9: 2522–2545. DOI: 10.1093/gbe/evx158 Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017b. Supplemental dataset for Northern Spotted Owl (Strix occidentalis caurina) genome assembly version 1.0. Zenodo. DOI: 10.5281/zenodo.822859 Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. 2017c. Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ. 5: e3901. DOI: 10.7717/peerj.3901

{"references": ["Hanna ZR., Henderson JB., Wall JD., Emerling CA., Fuchs J., Runckel C., Mindell DP., Bowie RCK., DeRisi JL., Dumbacher JP. 2017a. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biology and Evolution 9:2522\u20132545. DOI: 10.1093/gbe/evx158.", "Hanna ZR., Henderson JB., Wall JD., Emerling CA., Fuchs J., Runckel C., Mindell DP., Bowie RCK., DeRisi JL., Dumbacher JP. 2017b. Supplemental dataset for Northern Spotted Owl (Strix occidentalis caurina) genome assembly version 1.0. Zenodo. DOI: 10.5281/zenodo.822859.", "Hanna ZR., Henderson JB., Sellas AB., Fuchs J., Bowie RCK., Dumbacher JP. 2017c. Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 5:e3901. DOI: 10.7717/peerj.3901."]}