Supplementary Data for "Fast and Accurate Variant Identification Tool for Sequencing-Based Studies"

Benchmark datasets used in this study to evaluate the performance of QuickVariants and bcftools.Instruction of using these benchmark datasets can be found here.Gut_microbiome_benchmark.tar.gz contains gut microbiome WGS reads, original assembled genomes, and mutated genomes with in silico point mutations and indels. This dataset includes SRX5976902 Akkermansia muciniphila (A. muciniphila), SRX5977424 Bacteroides faecis (BaFa), SRX5976649 Bacteroides fragilis (B. fragilis), SRX5976729 Bacteroides ovatus (B. ovatus), SRX6045315 Bacteroides vulgatus (BaVu), SRX6044844 Bacteroides xylanisolvens (BaXy), SRX6044813 Bifidobacterium adolescentis (BiAd), SRX5991169 Escherichia coli (EsCo), and SRX5992782 Parabacteroides distasonis (PaDi).COVID_benchmark.tar.gz contains SARS-Cov-2 (NC_045512.2 and SRR10971381) WGS reads, original assembled genomes, and mutated genomes in silico point mutations and indels.WGS_simulation_sequencingerror.tar.gz contains illumine Hiseq 2500 and NextSeq 500 v2 WGS data simulated from a reference genome of B. fragilis NCTC 9343 (NCBI accession GCF_000025985.1) with sequencing error rates varying from 0.1 to 10 times the original error rate (-qs -10, -qs 1, and -qs 10).MG_simultation_sequencingerror.tar.gz contains an illumine Hiseq 2500 metagenomic dataset simulated from nine human gut microbiome reference genomes with the original sequencing error rate and 20X read depth.MGBIG_simultation_sequencingerror.tar.gz contains an illumine Hiseq 2500 metagenomic dataset simulated from nine human gut microbiome reference genomes with the original sequencing error rate and 100X read depth.COVID_MGSW.tar.gz contains three longitudinal metagenomes from Wisconsin, USA sewage, collected in January 2022 (NCBI Accession SRR21019653, SRR21019687) and March 2023 (NCBI Accession SRR23934917), and SARS-Cov-2 reference genome (NC_045512.2).ExampleDataFig4-6.zip contains sam and vcf output files that support the examples shown in Fig 4-6.