Anchored Hybrid Enrichment Bioinformatic Files for Tuber rufum Phylogenetic Analysis

All analysis pipelines and visualisation scripts are avaliable at Tuber_Phylogenomics_GitHub All raw reads for which assemblies were generated and gene predicition ran are avaliable at PRJNA1327327 prok_viral_filters.tar.gz - Combined prokaryotic and viral filters for each sample at 100 and 200 bit scores. raxml_iqtree.tar.gz - All files for the Proteinortho -> RAxML phylogenomic tree, and all files for the Proteinortho -> IQTree restimation analyses. This also include custom python and perl programs used. viral_blast.tar.gz - Viral blast results for all samples (including filtering at 100 and 200 bit scores). prok_blast.tar.gz - Prokaryotic blast results for all samples (including filtering at 100 and 200 bit scores). multiqc_report.html - Multiqc report for the raw reads and trimmed reads. Tuly_Filtered_exons.fasta - Exons used for DNA capture probe design. busco_summary.tsv - Results from BUSCO analyses run on assemblies for all samples. funannotate_summary.tsv - Results for all samples for gene prediction. gene_prediction.tar.gz - All predicted genes from the funannotate pipeline for the 100 and 200 bit score assemblies. This also includes the assembly fastas used in gene predicition, as well as the additional protein evidence downloaded and used.