The data presented here are for the manuscript "Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens" by Saeidi et al. 2018 published in JoVE. All analyses were conducted using Illumina 2x150 reads for the herbarium specimen Schizachyrium_scoparium-TK686 and its re-amplified library Schizachyrium_scoparium-TK686R. Directory: Chloroplast_Assembly Directory: Schizachyrium_scoparium-TK686 Contents: Output directory hierarchy from Fast-Plast for chloroplast assembly. Directory: Schizachyrium_scoparium-TK686R Contents: Output directory hierarchy from Fast-Plast for chloroplast assembly. Directory: Fungal_Contamination File: bulk_download_JGI.pl Contents: Script for bulk download of fungal mitochondrial and nuclear genomes. Use: perl bulk_download_JGI.pl MycoCosm_Download_Info.txt File: Genomes_used_for_Mitochondrial_Contamination_DB.txt Contents: List of mitochondrial genomes by species and version. File: Genomes_used_for_Nuclear_Contamination_DB.txt Contents: List of nuclear genomes by species and version. File: get_db_genomes_used.pl Contents: Script used to generate list of mitochondrial and nuclear genomes used for database. File: make_fungal_db.pl Contents: Script to combine mitochondrial and nuclear genome sequences into different files. Use: perl make_fungal_db.pl Nuclear (for nuclear genomes) and perl make_fungal_db.pl Mito (for mitchondrial genomes). Must have all files in the same directory that are gzipped (as downloaded from MycoCosm). File: MycoCosm_Download_Info.txt Contents: File information from Phytozome for all fungal mitochondrial and nuclear genomes used for database. Directory: GC_Content File: get_gc_all_files.pl Contents: Perl script for retrieving GC content from FASTA files. Script is hard coded for specific directories and file names. Will need to altered for other users. File: GC_content_all_andropogoneae.txt Contents: %GC, %AT, and total basepairs for two Schizachyrium scoparium TK686 datasets used in manuscript. Directory: Transposons Directory: Schizachyrium_scoparium-TK686 Contents: One hundred 100,000 read subsets from total read data for sample TK686 with each yml control file and condor submission file for Transposome runs. Also includes Transposome output directories. Each directory includes all Transposome output files. Directory: Schizachyrium_scoparium-TK686R Contents: One hundred 100,000 read subsets from total read data for sample TK686R with each yml control file and condor submission file for Transposome runs. Also includes Transposome output directories. Each directory includes all Transposome output files. File: pull_annotations_transposome_average.pl Contents: Script for getting average and standard deviation from Transposome bootstraps. To run, perl pull_annotations_transposome_average.pl File_list_of_Directories_one_per_line Prefix_output. File: TE_annotation_results_average.txt Contents: Average percent of reads for each identified transposon superfamily or repeat type. This is out of 100 subsets of 100,000 reads from total read set. Values calculated from the Transposome output file Schizachyrium_scoparium-TK686_t_cluster_report_annotations_summary.tsv or Schizachyrium_scoparium-TK686R_t_cluster_report_annotations_summary.tsv for each data set. File: TE_annotation_results_stdev.txt Contents: Standard deviation of percent of reads for each identified transposon superfamily or repeat type. This is out of 100 subsets of 100,000 reads from total read set. Values calculated from the Transposome output file Schizachyrium_scoparium-TK686_t_cluster_report_annotations_summary.tsv or Schizachyrium_scoparium-TK686R_t_cluster_report_annotations_summary.tsv for each data set.