Supplemental Results for Assembly, Annotation, and Analysis from HiFi reads of Gulf Toadfish Genome and Transcriptome fOpsBet2.1

This repository contains gzipped tarballs of the results of the various assembly, annotation, and analysis steps performed during the assembly of the fOpsBet2.1 genome assembly for Opsanus beta at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science for the McDonald Toadfish Lab. These results are too numerous to include as supplemental data for a journal publication and so are available here for review. In this repository you will find results for:
Scripts:
-all bash and LSF scheduler job scripts used as part of the analysis, both exploratory and final. 
QC:
-GenomeScope2 estimation of genome metrics from HiFi Reads
-QUAST genome statistics for each assembly step
-BUSCO completeness assessments for each assembly step 
-inspector logs for polishing of initial assembly
-logs from Kraken2 contaminant screen
Assembly and Scaffolding:
-ntLINKS logs and intermediates for initial scaffolding
-ragtag logs and metrics for super-scaffolding to the ThaAma1.1 T. amazonica reference assembly
-mitoHIFI results for mitogenome assembly from HiFi reads, primary assembly, and purged alternate assembly
Annotation:
-PASA directory with full input and output for SQLite PASA assembly of transcriptome for gene predictors
-Results folder for Funannotate::annotate for gene models, annotations, and CDS/mRNA/protein fastas
-InterProSCan5 results for protein annotation used as input into Funannotate
-ghostKOALA KEGG assignment results for predicted proteins from funannotate results
Repetitive Elements:
-tidk telomere repeat analysis results
-TRAH satellite DNA analysis with subsequent analysis with HiCAT and StainedGlass
-RepeatModeler results for de novo TE prediction
-repclassifier results for TE curation
Comparative Analysis:
-OrthoFinder ortholog search for O. beta to several other vertebrates
-CAFE5 gene family expansion and contraction of Orthogroups from OrthoFinder results