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
Language:Nextflow417 14 51672
assembly-scan
Generate basic stats for an assembly.
Language:Python9 3 00
camlhmp
🐪Classification through yAML Heuristic Mapping Protocol 🐪
Language:Python8 1 52
dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
Language:Perl117 4 3510
fastq-dl
Download FASTQ files from SRA or ENA repositories.
Language:Python277 5 1725
fastq-scan
Output FASTQ summary statistics in JSON format
Language:C++29 3 51
pasty
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
Language:Shell11 3 21
pbptyper
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
Language:Python9 2 10
sccmec
A tool for typing SCCmec cassettes in assemblies
Language:Python2 2 00
vcf-annotator
Add biological annotations to variants in a given VCF file.
Language:Python26 4 87

rpetit3's Repositories

rpetit3/vcf-annotator
Add biological annotations to variants in a given VCF file.
Language:Python26 4 87
rpetit3/illumina-cleanup
A simple pipeline for pre-processing Illumina FASTQ files.
Language:Nextflow3 3 32
rpetit3/pmga
A command-line version of PMGA (PubMLST Genome Annotator) for serogrouping and serotyping of all Neisseria species and Haemophilus influenzae
Language:Python1 2 1
rpetit3/shovill
A fork of Shovill that includes support for single end reads.
Language:Perl1 3 01
rpetit3/bactopia
A flexible pipeline for complete analysis of bacterial genomes
Language:Nextflow2 0
rpetit3/Bio-Easel
Perl modules and scripts for interfacing with Sean Eddy's C easel sequence analysis library using Perl's Inline.
Language:Perl
rpetit3/clinker
Gene cluster comparison figure generator
Language:Python2 01
rpetit3/CSIS
Code Safety Inspection Service
2 0
rpetit3/docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Language:Dockerfile2 0
rpetit3/github-style
Language:CSS2 0
rpetit3/hAMRoaster
hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance
Language:Python2 01
rpetit3/hicap
👋🎓 in silico typing of the H. influenzae cap locus
Language:Python2 0
rpetit3/Kleborate
Language:Python1 0
rpetit3/legsta
🍗⭐ In silico Legionella pneumophila Sequence Based Typing
rpetit3/LMAS
LMAS - Last (Meta)Genomic Assembler Standing
Language:Python2 0
rpetit3/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
rpetit3/nf-validation
Params validation plugin for Nextflow pipelines
rpetit3/nonpareil
Estimate metagenomic coverage and sequence diversity
Language:C++1 0
rpetit3/phirbo
Predict prokaryotic hosts for phage (meta) genomic sequences
Language:Python2 0
rpetit3/pipeline-resources
Bioinformatics Pipeline and Visualization resources
rpetit3/rpetit3
2 0
rpetit3/spaTyper
Computational method for finding spa types.
Language:Python2 0
rpetit3/staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
Language:Nextflow2 0
rpetit3/taxprofiler
Taxonomic profiling of shotgun metagenomic data
rpetit3/tools
Python package with helper tools for the nf-core community.
Language:Python2 0
rpetit3/ultraplex
Ultra-fast 5' and 3' demultiplexer
rpetit3/utterances
:crystal_ball: A lightweight comments widget built on GitHub issues
Language:TypeScript2 0
rpetit3/vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
Language:Perl2 0
rpetit3/vadr-extra
Files related to vadr that don't belong in the main repo.
2 0
rpetit3/workflows-wdl
A set of WDL workflows (mostly workflows of workflows).
Language:WDL3 0