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本仓库包含迈阿密大学罗森斯蒂尔海洋、大气与地球科学学院麦当劳蟾鱼实验室开展的斑蟾鱼（Opsanus beta）fOpsBet2.1基因组组装流程中，各类组装、注释与分析步骤所得结果的gzip压缩tar包。此类结果数量繁多，无法作为期刊论文的补充数据公开，因此在此处供同行审阅。本仓库涵盖以下分析结果： 脚本： - 用于本次分析的全部Bash脚本与LSF调度器作业脚本，涵盖探索性分析与最终分析脚本。 质量控制： - 基于HiFi测序reads的GenomeScope2基因组参数估算结果 - 各组装步骤的QUAST基因组统计信息 - 各组装步骤的BUSCO（Benchmarking Universal Single-Copy Orthologs）完整性评估结果 - 初始组装基因组抛光（polishing）的Inspector日志 - Kraken2污染物筛查日志 组装与支架构建： - ntLINKS初始支架构建的日志与中间文件 - 以ThaAma1.1版本的亚马逊鲶鱼（T. amazonica）参考基因组为参照的ragtag超级支架构建日志与评估指标 - 基于HiFi reads的线粒体基因组组装mitoHIFI结果，包含原始组装与经去重的替代组装 基因注释： - PASA（Program to Assemble Spliced Alignments）目录：包含用于基因预测的转录组SQLite PASA组装的全部输入与输出文件 - Funannotate::annotate结果文件夹：涵盖基因模型、注释信息以及CDS/mRNA/蛋白质FASTA文件 - InterProScan5蛋白质注释结果，作为Funannotate的输入数据 - 基于funannotate预测蛋白的ghostKOALA KEGG功能注释结果 重复序列分析： - tidk端粒重复序列分析结果 - TRAH卫星DNA分析结果，以及后续基于HiCAT与StainedGlass的分析结果 - RepeatModeler从头转座因子（Transposable Element, TE）预测结果 - repclassifier转座因子注释结果 比较基因组分析： - OrthoFinder直系同源搜索分析：针对斑蟾鱼（O. beta）与其他数种脊椎动物 - 基于OrthoFinder所得直系同源基因簇（Orthogroups）的CAFE5基因家族扩张与收缩分析