Data from: Evaluation of reference genome quality and phylogenetic distance for population genomic inference from low-coverage WGS data.

Contents of data repository for Voges et al. Evaluation of reference genome quality and phylogenetic distance for population genomic inference from low-coverage WGS data. For further details refer to the methodology outlined in the article. 1_References_from_Voges_et_al_2027_Reference_Genome_Quality.zip Containing two subfolders with assembled references following the terminology as in Voges et al. 1.1_Long-read_references: Folder containing the long-read assemblies for 1_LR-con_ref.fasta and 2_LR-sp_ref.fasta 1.2_Short-read_references: Folder containing the short-read assemblies 3_SR-sp_ref.fasta and 4_SR-sis_ref.fasta 2_IlluminaRAWreads_from_Voges_et_al_2027_Reference_Genome_Quality.zip Folder containing Illumina RAW reads for all 15 taxa analyzed in the study. 3_MappingStats_ from_Voges_et_al_2027_Reference_Genome_Quality.zip Folder containing statistical test results as described in Methods from Voges et al. for the mapping performance of each individual as .csv or .txt files. 4_SNPs_from_Voges_et_al_2027_Reference_Genome_Quality.zip Containing two subfolders, one per filtering strategy 4.1_strictfilters: Folder containing the .arg and .mafs.gz files per reference with SNPs for the filtered dataset as described in Methods 4.2_relaxedfilters: Folder containing the .arg and .mafs.gz files per reference with SNPs for the unfiltered dataset as described in Methods 5_PCAngsd_from_Voges_et_al_2027_Reference_Genome_Quality.zip Containing two subfolders, one per filtering strategy 5.1_strictfilters: Folder containing the .cov files with the covariance matrices for each reference under strict filtering scheme used in the PCA analysis 5.2_relaxedfilters: Folder containing the .cov files with the covariance matrices for each reference under relaxed filtering scheme used in the PCA analysis 6_NGSadmix_from_Voges_et_al_2027_Reference_Genome_Quality.zip Containing two subfolders, one per filtering strategy 6.1_strictfilters: Folder containing three subfolders with the data based on the filtered dataset used in the NGSadmix analysis 6.1.1_ngsadmix: contains .qopt and .log files for each K and replication from the NGSadmix analysis. It also contains .csv and .tsv files with the statistical comparison data. 6.1.2_consensus: contains the .qopt and .info.tsv files for each reference and consensus file per K. 6.1.3_evalAdmix_best_replicates: contains the .evalAdmix file for the best replicate per reference and K. 6.2_relaxedfilters: Folder containing three subfolders with the data based on the unfiltered dataset used in the NGSadmix analysis 6.1.1_ngsadmix: contains .qopt and .log files for each K and replication from the NGSadmix analysis. It also contains .csv and .tsv files with the statistical comparison data. 6.1.2_consensus: contains the .qopt and .info.tsv files for each reference and consensus file per K. 7_GeneticDiversity_from_Voges_et_al_2027_Reference_Genome_Quality.zip 7.1_strictfilters: Folder containing four subfolders corresponding to the three genetic diversity parameters (fst, pi and Ho) measured in the study and one folder containing the statistical estimates described in the study, calculated based on the filtered dataset. 7.1.1_fst: Containing the folded.2dsds and folded.fst.idx files per reference and population comparison. 7.1.2_pi: Containing the folded.sfs and folded.thetas.idx files per reference and population. 7.1.3_ho: Containing the .arg, .folded.sfs, .saf.idx, and .tsv files per reference and individual. 7.1.4_statistics_fst_pi_ho: containing .csv, and .txt files with the statistical estimates for each genetic diversity parameter as described in Voges et al. 7.2_relaxedfilters: Folder containing four subfolders corresponding to the three genetic diversity parameters (fst, pi and Ho) measured in the study and one folder containing the statistical estimates described in the study, calculated under the relaxed filtering scheme. 7.2.1_fst: Containing the folded.2dsds and folded.fst.idx files per reference and population comparison. 7.2.2_pi: Containing the folded.sfs and folded.thetas.idx files per reference and population. 7.2.3_ho: Containing the .arg, .folded.sfs, .saf.idx, and .tsv files per reference and individual. 7.2.4_statistics_fst_pi_ho: containing .csv, and .txt files with the statistical estimates for each genetic diversity parameter as described in Voges et al.