https://www.robertpetit.com/tags/tools/Recent content in Tools on Robert A. Petit III, PhDHugoen-us&copy; Dr. Robert A. Petit III, 2020-{year}Sat, 14 Nov 2026 03:53:12 +0000https://www.robertpetit.com/publication/2026-camlhmp-simple-framework-building-reproducible-microbial-genome/Mon, 20 Apr 2026 00:00:00 +0000https://www.robertpetit.com/publication/2026-camlhmp-simple-framework-building-reproducible-microbial-genome/Sequence-based typing is critical for microbial genomics, yet existing tools are often developed in isolation, leading to duplicated effort, inconsistent formats, and limited community participation.https://www.robertpetit.com/publication/2025-camp-modular-metagenomics-analysis-system-integrated-multistep-data/Thu, 30 Oct 2025 00:00:00 +0000https://www.robertpetit.com/publication/2025-camp-modular-metagenomics-analysis-system-integrated-multistep-data/Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities.https://www.robertpetit.com/publication/2023-accelerating-bioinformatics-implementation-public-health/Mon, 10 Jul 2023 00:00:00 +0000https://www.robertpetit.com/publication/2023-accelerating-bioinformatics-implementation-public-health/We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs).https://www.robertpetit.com/publication/2021-pollen-id/Thu, 04 Nov 2021 00:00:00 +0000https://www.robertpetit.com/publication/2021-pollen-id/We report comparisons between WGS and DNA metabarcoding for plant species identification.https://www.robertpetit.com/software/any2tsv/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/any2tsv/Convert various bioinformatic outputs to TSVhttps://www.robertpetit.com/software/assembly-scan/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/assembly-scan/Generate basic stats for an assemblyhttps://www.robertpetit.com/software/bactopia-py/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/bactopia-py/A Python package for working with Bactopiahttps://www.robertpetit.com/software/bactopia-wdl/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/bactopia-wdl/A WDL wrapper around Bactopiahttps://www.robertpetit.com/software/camlhmp/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/camlhmp/Classification through YAML Heuristic Mapping Protocolhttps://www.robertpetit.com/software/dragonflye/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/dragonflye/Assemble bacterial isolate genomes from Nanopore readshttps://www.robertpetit.com/software/genome-dl/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/genome-dl/Download genomes from NCBI Datasetshttps://www.robertpetit.com/software/goblin/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/goblin/GOBLIN - Generate trusted prOteins to supplement BacteriaL annotatIoNhttps://www.robertpetit.com/software/nf-bactopia/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/nf-bactopia/A Nextflow plugin for Bactopiahttps://www.robertpetit.com/software/pasty/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/pasty/A tool easily taken advantage of for in silico serogrouping of <em>Pseudomonas aeruginosa</em> isolateshttps://www.robertpetit.com/software/pbptyper/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/pbptyper/In silico Penicillin Binding Protein (PBP) typer for <em>Streptococcus pneumoniae</em> assemblieshttps://www.robertpetit.com/software/pmga/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/pmga/A fork of PMGA (PubMLST Genome Annotator) for all <em>Neisseria</em> species and <em>Haemophilus influenzae</em>https://www.robertpetit.com/software/s3tools/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/s3tools/Simple S3 scripts using Boto for Staphopiahttps://www.robertpetit.com/software/sizemeup/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/sizemeup/A simple tool to determine the genome size of an organismhttps://www.robertpetit.com/software/staphopia-r/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/staphopia-r/An R library to extract data from Staphopia&rsquo;s API (archived)https://www.robertpetit.com/software/steamboat-py/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/steamboat-py/A collection of tools and scripts for microbial bioinformaticshttps://www.robertpetit.com/software/tbl2asn-forever/Mon, 01 Jan 0001 00:00:00 +0000https://www.robertpetit.com/software/tbl2asn-forever/A fork of tbl2asn-forever available from Bioconda