Read-Me file for mitogenome assembly pipeline scripts, SNP discovery pipeline scripts, and SNP genotype data extraction script. Files: ngs-mtdna-pipeline-v3.2.r ngs-snp-pipeline-v3.2.r ngs.funcs.rdata merged vcf to genotype.r The R script ngs-mtdna-pipeline-v3.2.r uses a series of publicly available software packages (described in the text) to trim, assemble, and align mitogenome read data from a set of FASTQ files in a folder to a reference mitochondrial DNA sequence FASTA file, using a Linux platform. The scripts also make use of the Rdata file ?ngs.funcs.rdata?, and several required R packages, described in the script comments. Parameters of the assembly can be altered in the pipeline script. Installation of required software and R packages is required prior to running the script, as well as appropriate selection of the input FASTQ data folder. The R script ngs-SNP-pipeline-v3.2.r uses a series of publicly available software packages (described in the text) to trim, assemble, and align nuclear locus read data from a set of FASTQ files in a folder to a reference set of nuclear DNA sequences in a FASTA file, using a Linux platform. The scripts also make use of the Rdata file ?ngs.funcs.rdata?, and several required R packages, described in the script comments. Parameters of the assembly can be altered in the pipeline script. Installation of required software and R packages is required prior to running the script, as well as appropriate selection of the input FASTQ data folder. The R script ?merged vcf to genotype.r? can be run as a stand-alone R-script from the SNP data output directory generated by ?ngs-snp-pipeline-v3.2.r?. It requires several R packages to run, and compiles the SNP read data from the output folder ?vcf? into a .csv file with columns for called genotypes and number of reads for each sample and SNP locus. This output file can be put into a database (e.g., Access) and queried to identify genotypes for individual samples at each locus (e.g., for SNP verification or for ?genotyping by sequencing?).