Supplementary Data for "<b>Fast and Accurate Variant Identification Tool for Sequencing-Based Studies</b>"
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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 <i>in silico</i> point mutations and indels. This dataset includes SRX5976902 <i>Akkermansia muciniphila</i> (<i>A. muciniphila</i>), SRX5977424 <i>Bacteroides</i><i> </i>faecis (<i>BaFa</i>), SRX5976649 <i>Bacteroides fragilis</i> (<i>B. fragilis</i>), SRX5976729 <i>Bacteroides ovatus</i> (<i>B. ovatus</i>), SRX6045315 <i>Bacteroides vulgatus</i> (<i>BaVu</i>), SRX6044844 <i>Bacteroides xylanisolvens</i><i> </i>(<i>BaXy</i>), SRX6044813 <i>Bifidobacterium adolescentis</i> (<i>BiAd</i>), SRX5991169 <i>Escherichia coli</i><i> </i>(<i>EsCo</i>), and SRX5992782 <i>Parabacteroides distasonis</i> (<i>PaDi</i>).COVID_benchmark.tar.gz contains SARS-Cov-2 (NC_045512.2 and SRR10971381) WGS reads, original assembled genomes, and mutated genomes <i>in silico</i> 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 <i>B. fragilis</i> 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.
