rpetit3

fastq-dl

Download FASTQ files from SRA or ENA repositories.

dragonflye

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

pasty

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

primerForge

software to identify primers that can distinguish genomes

camlhmp

🐪Classification through yAML Heuristic Mapping Protocol 🐪

illumina-cleanup

A simple pipeline for pre-processing Illumina FASTQ files.

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

admin

basic scripts for server administration

robertpetit.com

My personal site

sccmec

A tool for typing SCCmec cassettes in assemblies

seqbox

local sequence management lightweight tools

sizemeup

A simple tool to determine the genome size of an organism

steamboat-py

A collection of tools/scripts for microbial bioinformatics

aquascope

bioconda-recipes

Conda recipes for the bioconda channel.

configs

Config files used to define parameters specific to compute environments at different Institutions

czgenepi

django-steamboat

A custom sequence information management system powered by Django

github-graphql-action

An action which executes graphql queries

hicap

👋🎓 in silico typing of the H. influenzae cap locus

lskatz.github.io

Website for Lee Katz

medaka

Sequence correction provided by ONT Research

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

server

:sailboat: LandSandBoat - a server emulator for Final Fantasy XI. Just an X-34 landspeeder out for a drive.

skel

Some useful skeleton files

sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

test-security

temporary repository to test security settings

ubinfie.github.io

µbinfie blog

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples