Guppy and M. picta repeats_annotation

The dataset was produced using RepeatModeler2 (Flynn et al. 2020) to generate an initial comprehensive set of candidate TE families in the male reference genome assembly (Fraser et al. 2020). RepeatMasker (Smit et al. http:// repeatmasker.org) was used to make a library of consensus sequences from the RepeatModeler2 analysis plus Teleostei repeats from Repbase (https://www.girinst.org/repbase/). A filtered list of candidates was created and manually annotated following the procedures and criteria described by Goubert et al. (2022). RepeatMasker was then run again to find and annotate repeat copies throughout the male reference genome. 2. There are two files with results from the guppy, , as follows. GUPPY_consensus_library.fa (consensus TE library from RepeatModeler) guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result) 3. Micropoecilia picta: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly. Files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly For the whole genome picta_assembly.unmasked.out picta_assembly.unmasked.out.gff For just chromosome 12, the sex chromosome LG12_picta.fa.out LG12_picta.fa.out.gff The consensus sequences produced by RepeatModeler consensi_picta.fa.classified consensi.fa References Flynn, J. M., R. Hubley, C. Goubert, J. Rosen, A. G. Clark et al., 2020 RepeatModeler2: automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117: 9451-9457. doi: 10.1073/pnas.1921046117 Fraser, B. A., J. R. Whiting, J. R. Paris, C. J. Weadick, P. J. Parsons et al., 2020 Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biology and Evolution 12: 1789–1805. doi: 10.1093/gbe/evaa187 Goubert, C., R. J. Craig, A. F. Bilat, V. Peona, A. A. Vogan et al., 2022 A beginner's guide to manual curation of transposable elements. Mob DNA 13: 7. doi: 10.1186/s13100-021-00259-7 Smit, A., R. Hubley and P. Green, 2013-2015 RepeatMasker Open-4.0<br>1. There are two files with results from the guppy, as follows.GUPPY_consensus_library.fa (consensus TE library from RepeatModeler)guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result)<br>2. <i>Micropoecilia picta</i>: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly.<br>Files from the RepeatModeler and RepeatMasker analyses of the M. picta assemblyFor the whole genomepicta_assembly.unmasked.outpicta_assembly.unmasked.out.gff<br>For just chromosome 12, the sex chromosomeLG12_picta.fa.outLG12_picta.fa.out.gff<br>The consensus sequences produced by RepeatModelerconsensi_picta.fa.classifiedconsensi.fa<br>