Sequencing on Robert A. Petit III, PhDhttps://www.robertpetit.com/tags/sequencing/Recent content in Sequencing on Robert A. Petit III, PhDHugoen-us&copy; Dr. Robert A. Petit III, 2020-{year}Sat, 14 Nov 2026 03:53:12 +0000Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applicationshttps://www.robertpetit.com/publication/2023-putting-everything-its-place-using-insdc-compliant-pathogen-data/Tue, 12 Dec 2023 00:00:00 +0000https://www.robertpetit.com/publication/2023-putting-everything-its-place-using-insdc-compliant-pathogen-data/Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge.Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways.https://www.robertpetit.com/publication/2023-oman-tb/Thu, 28 Sep 2023 00:00:00 +0000https://www.robertpetit.com/publication/2023-oman-tb/We report evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman.Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in *Staphylococcus aureus* strainshttps://www.robertpetit.com/publication/2023-saureus-amplicon/Mon, 23 Jan 2023 00:00:00 +0000https://www.robertpetit.com/publication/2023-saureus-amplicon/We report direct <em>S. aureus</em> antibiotic resistance genotype inference using rapid nanopore sequencing from clinical samplesShiftwork, functional bowel symptoms, and the microbiomehttps://www.robertpetit.com/publication/2021-shiftwork/Tue, 11 May 2021 00:00:00 +0000https://www.robertpetit.com/publication/2021-shiftwork/We report the effects of shiftwork on the intestinal microbiome.Whole-Genome Sequences of *Staphylococcus aureus* Isolates from Cystic Fibrosis Lung Infectionshttps://www.robertpetit.com/publication/2019-saureus-cf-mra/Tue, 01 Jan 2019 00:00:00 +0000https://www.robertpetit.com/publication/2019-saureus-cf-mra/we present the whole-genome sequences of 65 Staphylococcus aureus isolates obtained from 50 individuals with cystic fibrosis.bactopia-qchttps://www.robertpetit.com/software/bactopia-qc/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/bactopia-qc/The methods used in Bactopia for read QCena-dlhttps://www.robertpetit.com/software/ena-dl/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/ena-dl/Download FASTQ files from ENA (archived)fastq-dlhttps://www.robertpetit.com/software/fastq-dl/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/fastq-dl/Download FASTQ files from SRA or ENA repositories.fastq-scanhttps://www.robertpetit.com/software/fastq-scan/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/fastq-scan/Output FASTQ summary statistics in JSON formatgenome-dlhttps://www.robertpetit.com/software/genome-dl/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/genome-dl/Download genomes from NCBI Datasetsillumina-cleanuphttps://www.robertpetit.com/software/illumina-cleanup/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/illumina-cleanup/A Nextflow pipeline for pre-processing Illumina FASTQ filesillumina-simulationhttps://www.robertpetit.com/software/illumina-simulation/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/illumina-simulation/Dockerized Illumina sequencing simulation and 31-mer counting using ART and Jellyfishshovill-sehttps://www.robertpetit.com/software/shovill-se/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/shovill-se/A fork of Shovill that includes support for single end readsvcf-annotatorhttps://www.robertpetit.com/software/vcf-annotator/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/vcf-annotator/Add biological annotations to variants in a given VCF file.