esteinig

Bioinformatics | Infectious Diseases | Nanopore | Metagenomic Diagnostics | Software Development

Victorian Infectious Disease Reference Laboratory (VIDRL), The Peter Doherty Institute for Infection and Immunity (PDI)Melbourne, Australia

Pinned Repositories

achilles
Artificial neural networks for taxonomic nanopore signal classification in host microbiomes *update soon* :deciduous_tree:
Language:Python7 2 232
brick
BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons :microbe:
Language:Svelte12 1 250
BRIGAD3
D3 and Vue component for visualization of bacterial genome assemblies from nanopore sequence data
Language:Python10 3 02
nanoq
Minimal but speedy quality control for nanopore reads in Rust :bear:
Language:Rust127 5 4210
netview
Mutual nearest neighbor graphs and data visualization for genomic population networks :octopus:
Language:R18 0 23
netviewP
NetView for Python
Language:Python8 4 32
netviewr
Mutual nearest neighbor graphs for population structure inference and visualization :octopus:
Language:Rust16 0 72
scrubby
Host depletion optimised for clinical metagenomic sequencing applications :panda_face:
Language:Rust14 2 172
sketchy
Genomic neighbor typing of bacterial pathogens using MinHash :rat:
Language:Rust44 7 543
vircov
Viral genome coverage evaluation for metagenomic diagnostics :drop_of_blood:
Language:Rust28 2 174

esteinig's Repositories

esteinig/BRIGAD3
D3 and Vue component for visualization of bacterial genome assemblies from nanopore sequence data
Language:Python10 3 02
esteinig/netviewP
NetView for Python
Language:Python8 4 32
esteinig/dartqc
Quality Control for DArT SNPs
Language:Python6 4 32
esteinig/thicket
Parallel bootstrapping for maximum-likelihood phylogenies wrapping RAxML-NG, PhyML and FastTree :herb:
3 1 0
esteinig/melioidosis
Language:Python2 2 0
esteinig/eager
A fully reproducible and state of the art ancient DNA analysis pipeline.
Language:Nextflow1 0 0
esteinig/pnodes
Pretty print pbsnodes for Torque/PBS.
Language:Python1 0 0
esteinig/SPANDx
SPANDx - Comparative genomics for next-generation haploid sequence data
Language:Perl1 0 01
esteinig/ARDaP
Language:Shell0 0
esteinig/chroma.js
JavaScript library for all kinds of color manipulations
Language:CoffeeScript
esteinig/cookiecutter
A command-line utility that creates projects from cookiecutters (project templates). E.g. Python package projects, jQuery plugin projects.
Language:Python
esteinig/docker-shields
Shields.io in a Docker image :whale:
Language:Dockerfile0 0
esteinig/enaBrowserTools
A collection of scripts to assist in the retrieval of data from the ENA Browser
Language:Python0 0
esteinig/geonet
Network Map Projections for R
Language:R0 0
esteinig/github-markdown-toc
Easy TOC creation for GitHub README.md
Language:Shell0 0
esteinig/Kleborate
Language:Python0 0
esteinig/krocus
Language:Python0 0
esteinig/lapdog
Language:Python0 0
esteinig/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Language:Nextflow0 0
esteinig/notes
Bioinformatics: Notes
1 0
esteinig/pathfinder
Python package to manage pipelines and data processing; command line interface :snake:
1 0
esteinig/rasusa
Randomly subsample sequencing reads to a specified coverage
Language:Rust0 0
esteinig/sawfish
Longtooth sawfish nanopore genome assembly workflows
2 0
esteinig/ST772
Emergence and global spread of a multidrug-resistant, community-associated MRSA lineage from the Indian subcontinent
Language:HTML1 0
esteinig/template
Application template for chapters and libraries for my PhD
Language:Vue1 01
esteinig/test
Testing Singularity on the JCU HPC
0 0
esteinig/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
Language:Python0 0
esteinig/Unicycler
hybrid assembly pipeline for bacterial genomes
Language:C++0 0
esteinig/vagrant-ubuntu-rserver
Vagrant box (Ubuntu 16.04) + RStudio Server
0 01
esteinig/vipr
Assembly and intrahost / low-frequency variant calling for viral samples
Language:Nextflow0 0