snvphyl_manuscript_synthetic_datasets.tar.gz

This package contains synthetic datasets used to evaluate the the SNVPhyl (http://snvphyl.readthedocs.io/) pipeline. This is divided into two separate datasets. Additional details on how these datasets were constructed are available at https://github.com/apetkau/snvphyl-validations. 1. e-coli-simulated-dataset: Simulated reads for evaluated SNVPhyl's SNV detection accuracy. Reads are based off of an E. Coli reference genome (NC_002695), plus two plasmids (NC_002128, NC_002127) which were concatenated into a single fasta file reference-genome/e_coli_sakai_w_plasmids.fasta. Random mutations were introduced to produce the variant genomes present in the genomes under variant-genomes/. Reads were simulated using ART Illumina (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/) to generate the fastq files in this directory. 2. salmonella-heidelberg-contamination: Simulated reads for evaluating SNVPhyl's performance in the presence of contamination from another genomic sample. Reads for the sample SH13-001 (BioSample: SAMN04334637) were downsampled and contaminated with SH12-001 (BioSample: SAMN04334627) at percentages of 5%, 10%, 20%, and 30%.