rpetit3/workshops

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rpetit3/workshops

rpetit3

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A repository of trainings and workshops

fastq-dl

Download FASTQ files from SRA or ENA repositories.

dragonflye

🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads

fastq-scan

Output FASTQ summary statistics in JSON format

vcf-annotator

Add biological annotations to variants in a given VCF file.

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

assembly-scan

Generate basic stats for an assembly.

camlhmp

🐪Classification through yAML Heuristic Mapping Protocol 🐪

illumina-cleanup

A simple pipeline for pre-processing Illumina FASTQ files.

goblin

GOBLIN - Generate trusted prOteins to supplement BacteriaL annotatIoN

sccmec

A tool for typing SCCmec cassettes in assemblies

any2tsv

Convert various bioinformatic outputs to TSV

call_variants

A ruffus pipeline to call variants following GATK best practices.

steamboat-py

A collection of tools/scripts for microbial bioinformatics

sizemeup

A simple tool to determine the genome size of an organism

StarCluster-Plugins

A few plugins created for Staphopia's StarCluster instances

django-kmer-test

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

fitbit-steps

Pull yesterday's total steps from FitBit

binf-scripts

Personal bioinformatic related scripts that need a home.

admin

basic scripts for server administration