drhchen

scripts

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

scripts

CNproScan

CNV detection for prokaryote genomes using NGS sequencing data

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

resequence

Bacterial variants(structural variant and single nucleotide variant) calling pipeline by short read NGS data

PaperBLAST

PaperBLAST: find papers about a protein or its homologs

staph_adaptation_paper

Scripts to analyse within-host evolution during S. aureus colonisation and infection

maskrc-svg

Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

itol.toolkit

Helper Functions for Interactive Tree Of Life (iTOL)

table2itol

Generating iToL annotations from Spreadsheet or CSV files

coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.

amr_pangenome

Pan-genome construction/analysis tools centered around PATRIC and antimicrobial resistance

genomegaMap

Within-species genome-wide dN/dS estimation from very many genomes

Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

staphylococcus-pseudintermedius

This repository contains all code used in Sawhney & Vargas et al. (2023).

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

Pactyper

Clone type prediction for WGS sequenced clinical bacterial isolates based on provided core genome.

reddog-nf

pipeline for read mapping, snp calling and annotation for bacterial genomes

proksee-cmd

Repo for Proksee Cmd Line Tools

PATO

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.

accnet

Within-person-evolution-of-Bacteroides-fragilis

fastq-dl

Download FASTQ files from SRA or ENA repositories.

MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

Klebsiella-assembly-species

a tool for assigning species to Klebsiella assemblies

regentrans

regentrans: R package for investigating regional pathogen transmission using genomic data

rigraph

igraph R package

KleTy

KleTy: Klebsiella genotyping for its core genome and plasmids

ST95

irida-plugin-snippy-phylogenomics

Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.