indexofire

PhyloTrace

PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.

pca-book

Source files for a book on Principal component analysis

bacLIFE

public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

SyntenyFinder

SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.

VPsero

rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes

AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

ecoli_serotyping

In silico prediction of E. coli serotype

vista

The Pathogenwatch Vibrio cholerae genotyping tool

ComfyUI

The most powerful and modular stable diffusion GUI, api and backend with a graph/nodes interface.

Grandeur

UPHL's Reference Free Pipeline

awk-hack-the-planet

Source code repo for Ben Porter (FreedomBen)'s free course on Awk (originally a talk at Linux Fest Northwest 2019 and 2020)

assembly_accuracy

tools for assessing the accuracy of genome assemblies

fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:

genomad

geNomad: Identification of mobile genetic elements

dnaapler

Reorients assembled microbial sequences

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

rerio

Research release basecalling models and configurations

dragonflye

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

pairsnp

A set of scripts for calculating pairwise SNP distance

Qiime2-Microbiome-workshop

gravis

Interactive graph visualizations with Python and HTML/CSS/JS.

genomics_adventure

Workshop on Genomics - Genomics Adventure

awesome-nanopore

A curated list of awesome nanopore analysis tools.

appwrite

Your backend, minus the hassle.

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

ShigaPass

An in silico tool to predict Shigella serotypes

nfvibrio

Nextflow pipeline to run metagenomic sequence analysis of Vibrio Parahaemolyticus, based on nf-core template, by John Palmer & Zohaib Anwar

fastq-dl

Download FASTQ files from SRA or ENA repositories.