rpetit3
Bioinformatician at the Wyoming Public Health Laboratory. Developer of the Bactopia and other microbial genomic tools.
Wyoming Public Health LaboratoryCheyenne, WY
Pinned Repositories
bactopia
A flexible pipeline for complete analysis of bacterial genomes
assembly-scan
Generate basic stats for an assembly.
camlhmp
🐪Classification through yAML Heuristic Mapping Protocol 🐪
dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
fastq-dl
Download FASTQ files from SRA or ENA repositories.
fastq-scan
Output FASTQ summary statistics in JSON format
pasty
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
pbptyper
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
sccmec
A tool for typing SCCmec cassettes in assemblies
vcf-annotator
Add biological annotations to variants in a given VCF file.
rpetit3's Repositories
rpetit3/fastq-dl
Download FASTQ files from SRA or ENA repositories.
rpetit3/dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
rpetit3/pasty
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
rpetit3/pbptyper
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
rpetit3/camlhmp
🐪Classification through yAML Heuristic Mapping Protocol 🐪
rpetit3/primerForge
software to identify primers that can distinguish genomes
rpetit3/illumina-cleanup
A simple pipeline for pre-processing Illumina FASTQ files.
rpetit3/sccmec
A tool for typing SCCmec cassettes in assemblies
rpetit3/admin
basic scripts for server administration
rpetit3/robertpetit.com
My personal site
rpetit3/seqbox
local sequence management lightweight tools
rpetit3/sizemeup
A simple tool to determine the genome size of an organism
rpetit3/steamboat-py
A collection of tools/scripts for microbial bioinformatics
rpetit3/aquascope
rpetit3/bactopia
A flexible pipeline for complete analysis of bacterial genomes
rpetit3/bioconda-recipes
Conda recipes for the bioconda channel.
rpetit3/Cecret
Reference-based consensus creation
rpetit3/ClermonTyping
Clermont PCR method In-Silico
rpetit3/configs
Config files used to define parameters specific to compute environments at different Institutions
rpetit3/czgenepi
rpetit3/django-steamboat
A custom sequence information management system powered by Django
rpetit3/executor-feedstock
A conda-smithy repository for executor.
rpetit3/hicap
👋🎓 in silico typing of the H. influenzae cap locus
rpetit3/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
rpetit3/polaris
Coming soon
rpetit3/rpetit3
rpetit3/server
:sailboat: LandSandBoat - a server emulator for Final Fantasy XI. Just an X-34 landspeeder out for a drive.
rpetit3/skel
Some useful skeleton files
rpetit3/ubinfie.github.io
µbinfie blog
rpetit3/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples