Cheyenne, WY

Robert A. Petit III

Elite
@rpetit3

Bioinformatician at the Wyoming Public Health Laboratory. Developer of the Bactopia and other microbial genomic tools.

www.robertpetit.com/

fastq-dl. Download FASTQ files from SRA or ENA repositories.

401

dragonflye. :dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

136

vcf-annotator. Add biological annotations to variants in a given VCF file.

33

fastq-scan. Output FASTQ summary statistics in JSON format

29

pasty. A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates

15

assembly-scan. Generate basic stats for an assembly.

13

sccmec. A tool for typing SCCmec cassettes in assemblies

13

pbptyper. In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies

10

camlhmp. 🐪Classification through yAML Heuristic Mapping Protocol 🐪

9

primerForge. software to identify primers that can distinguish genomes

4

write-the. AI-powered Documentation and Test Generation Tool

3

tbl2asn-forever. Use tbl2asn forever by pretending that it's still 2019

3

illumina-cleanup. A simple pipeline for pre-processing Illumina FASTQ files.

3

shigatyper. CFSAN Shigella Typing Pipeline

2

any2tsv. Convert various bioinformatic outputs to TSV

2

goblin. GOBLIN - Generate trusted prOteins to supplement BacteriaL annotatIoN

2

call_variants. A ruffus pipeline to call variants following GATK best practices.

2

tautyping. This pipeline identifies genes or genomic segments which most closely resemble the genome-wide phylogenetic signal of a given organism using the Kendall Tau rank correlation statistic

2

pmga. A command-line version of PMGA (PubMLST Genome Annotator) for serogrouping and serotyping of all Neisseria species and Haemophilus influenzae

2

ena-dl. Download FASTQ files from ENA

1

workshops. A repository of trainings and workshops

1

binf-scripts. Personal bioinformatic related scripts that need a home.

1

seqbox. local sequence management lightweight tools

1

StarCluster-Plugins. A few plugins created for Staphopia's StarCluster instances

1

fitbit-steps. Pull yesterday's total steps from FitBit

1

django-kmer-test. Tests to determine the most efficient way to store DNA k-mers.

1

admin. basic scripts for server administration

1

shovill. A fork of Shovill that includes support for single end reads.

1

sizemeup. A simple tool to determine the genome size of an organism

1

robertpetit.com. My personal site

1

steamboat-py. A collection of tools/scripts for microbial bioinformatics

1
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