indexofire

ComfyUI

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

appwrite

Your backend, minus the hassle.

awesome-genome-visualization

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

MetaPhlAn

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

fastq-dl

Download FASTQ files from SRA or ENA repositories.

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)

awesome-nanopore

A curated list of awesome nanopore analysis tools.

genomad

geNomad: Identification of mobile genetic elements

dragonflye

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

rerio

Research release basecalling models and configurations

gravis

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

dnaapler

Reorients assembled microbial sequences

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

AllTheBacteria

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

fujiplot

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

ecoli_serotyping

In silico prediction of E. coli serotype

pairsnp

A set of scripts for calculating pairwise SNP distance

assembly_accuracy

tools for assessing the accuracy of genome assemblies

public_health_bioinformatics

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

genomics_adventure

Workshop on Genomics - Genomics Adventure

pca-book

Source files for a book on Principal component analysis

Grandeur

UPHL's Reference Free Pipeline

bacLIFE

Qiime2-Microbiome-workshop

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

ShigaPass

An in silico tool to predict Shigella serotypes

vista

The Pathogenwatch Vibrio cholerae genotyping tool

PhyloTrace

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

nfvibrio

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