Repeat Modeler analysis for B. pensylvanicus

Repeatmasker/RepeatModeler Analysis was performed using Singularity dfam-tetools-latest.sif (from https://github.com/Dfam-consortium/TETools).<b>The repeat database was built with Repeatmasker:</b>BuildDatabase -name pens Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fastaRepeatModeler -database pens -threads 20 -LTRStruct<b>The Hymenoptera dfam database was fetched with</b>wget "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 &gt; Apidae-rm.fa<b>The Apidae repeat library was merged with the B pensylvanicus library output (pens_curated-families.fa) to create the </b><b>Apidae_pens-families-rm.fa</b><b> repeatmasker library.</b><b>RepeatMasker was run:</b>RepeatMasker -lib Apidae_pens-families-rm.fa -pa 16 -gff Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta<b>Subdirectory pens_repeatmodeler_figshare</b> contains repeatmodeler libraries, outputs from repeatmasker (masked genome fasta, gff, summary count tables, etc) and logs.<b>Subdirectory OtherSp </b>contains output summaries (.tbl) files for repeats in other Bombus species and their relevant species-specific RepeatModeler + Apidae dfam custom repeat libraries (.fa). <b>Subdirectory RepeatModelerLibsOnly </b>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)<br>