Drosophila willistoni genome annotation

Genome annotation of Drosophila willistoni de novo assembly using long reads. Protein coding genes were predicted with Funannotate. This software aligned proteins and transcripts from the Drosophila willistoni Flybase annotation against the assembly using minimap2, diamond and exonerate. It processed these hints to be included by augustus when predicting protein coding genes.

LncRNAs were identified by FEELnc using stranded ribodepleted RNA-seq libraries from ovaries, testes, male accessory glands and whole body samples. Additional lncRNAs were identified by mapping lncRNAs sequences downloaded from RNA central identified for Drosophila willistoni.

Ribosomal RNAs were predicted with RNAmmer; tRNAs, with tRNAscan2; and other miscellaneous ncRNA, with cmsearch and Rfam models.