Repeat Modeler analysis for B. pensylvanicus

Repeatmasker/RepeatModeler Analysis was performed using Singularity dfam-tetools-latest.sif (from https://github.com/Dfam-consortium/TETools).The repeat database was built with Repeatmasker:BuildDatabase -name pens Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fastaRepeatModeler -database pens -threads 20 -LTRStructThe Hymenoptera dfam database was fetched withwget "https://www.dfam.org/releases/current/families/FamDB/dfam38-1_full.0.h5.gz"wget "https://www.dfam.org/releases/current/families/FamDB/dfam38-1_full.7.h5.gz"wget "https://www.dfam.org/releases/current/families/FamDB/README.txt"famdb.py -i Libraries families --format fasta_name --include-class-in-name --ancestors --descendants 7458 > Apidae-rm.faThe Apidae repeat library was merged with the B pensylvanicus library output (pens_curated-families.fa) to create the Apidae_pens-families-rm.fa repeatmasker library.RepeatMasker was run:RepeatMasker -lib Apidae_pens-families-rm.fa -pa 16 -gff Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fastaSubdirectory pens_repeatmodeler_figshare contains repeatmodeler libraries, outputs from repeatmasker (masked genome fasta, gff, summary count tables, etc) and logs.Subdirectory OtherSp contains output summaries (.tbl) files for repeats in other Bombus species and their relevant species-specific RepeatModeler + Apidae dfam custom repeat libraries (.fa). Subdirectory RepeatModelerLibsOnly contains output summaries (.tbl) files for repeats for B. pensylvanicus and other Bombus species using ONLY their relevant species-specific RepeatModeler output as the custom repeat library (.fa) (without the Apidae dfam)