esteinig

nanoq

Minimal but speedy quality control for nanopore reads in Rust :bear:

sketchy

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

vircov

Viral genome coverage evaluation for metagenomic diagnostics :drop_of_blood:

netview

Mutual nearest neighbor graphs and data visualization for genomic population networks :octopus:

scrubby

Background depletion/extraction using k-mer and/or alignment methods :panda_face:

brick

BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons :microbe:

achilles

Artificial neural networks for taxonomic nanopore signal classification in host microbiomes *update soon* :deciduous_tree:

sccion

Genotyping toolkit and long-read assembly pipelines for Staphylococcus aureus *under construction* :grapes:

netviewr

Graph decorators for data and population structure visualization :octopus:

poremongo

Nanopore signal management and neural network training data compiler in MongoDB *update soon* :seedling:

nf-mvp

A minimum viable Nextflow pipeline (Bioinformatics Clinic)

ca-mrsa

Emergence of community-associated MRSA

machine

Welcome to the Machine

critter

BEAST models for pathogen transmission dynamics in Python

mpx-twist

Monkeypox analysis workflow for Twist Viral enrichment (PE Illumina)

beastiary

Real time and remote trace inspection with BEASTIARY.

bioconda-recipes

Conda recipes for the bioconda channel.

cerebro

Metagenomic diagnostics stack for low abundance sample types and clinical reporting

docs

dorado

Oxford Nanopore's Basecaller

fieldbioinformatics

ARTIC fieldbioinformatics modifications

Icarust

Minimal implementation of Icarust for tinkering and learning [do not use]

INSaFLU

INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based suite

japsa

Just Another JAva Package for Sequence Analysis

rase-outbreak-db

RASE database for typing the ST93 outbreaks in FNQ and PNG

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

tonic

Implements a dangerous configuration, not for general use

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

wf-artic

ARTIC SARS-CoV-2 workflow and reporting