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/nanoq
Minimal but speedy quality control for nanopore reads in Rust :bear:
Language:Rust127 5 4210
esteinig/sketchy
Genomic neighbor typing of bacterial pathogens using MinHash :rat:
Language:Rust44 7 543
esteinig/vircov
Viral genome coverage evaluation for metagenomic diagnostics :drop_of_blood:
Language:Rust28 2 174
esteinig/netview
Mutual nearest neighbor graphs and data visualization for genomic population networks :octopus:
Language:R18 0 23
esteinig/netviewr
Mutual nearest neighbor graphs for population structure inference and visualization :octopus:
Language:Rust16 0 72
esteinig/scrubby
Host depletion optimised for clinical metagenomic sequencing applications :panda_face:
Language:Rust14 2 172
esteinig/brick
BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons :microbe:
Language:Svelte12 1 250
esteinig/achilles
Artificial neural networks for taxonomic nanopore signal classification in host microbiomes *update soon* :deciduous_tree:
Language:Python7 2 232
esteinig/sccion
Genotyping toolkit and long-read assembly pipelines for Staphylococcus aureus *under construction* :grapes:
Language:Python7 0 83
esteinig/poremongo
Nanopore signal management and neural network training data compiler in MongoDB *update soon* :seedling:
Language:Python4 2 4
esteinig/nf-mvp
A minimum viable Nextflow pipeline (Bioinformatics Clinic)
Language:Nextflow3 1 01
esteinig/ca-mrsa
Emergence of community-associated MRSA
Language:R2 1 1
esteinig/cerebro
Metagenomic diagnostics stack for low abundance sample types and clinical reporting
Language:Rust2 2 18
esteinig/machine
Welcome to the Machine
Language:Python2 3 03
esteinig/critter
BEAST models for pathogen transmission dynamics in Python
Language:Python1 2 10
esteinig/mpx-twist
Monkeypox analysis workflow for Twist Viral enrichment (PE Illumina)
Language:Python0 1 03
esteinig/beastiary
Real time and remote trace inspection with BEASTIARY.
Language:Vue0 0
esteinig/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
esteinig/delphy
Fast, scalable, accurate and accessible Bayesian phylogenetics
Language:C++0 0
esteinig/docs
Language:HTML0 0
esteinig/dorado
Oxford Nanopore's Basecaller
Language:C++0 0
esteinig/fieldbioinformatics
ARTIC fieldbioinformatics modifications
Language:Python0 0
esteinig/Icarust
Minimal implementation of Icarust for tinkering and learning [do not use]
Language:Rust0 0
esteinig/INSaFLU
INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based suite
Language:HTML0 0
esteinig/japsa
Just Another JAva Package for Sequence Analysis
Language:Java0 0
esteinig/rase-outbreak-db
RASE database for typing the ST93 outbreaks in FNQ and PNG
Language:Python1 0
esteinig/recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Language:Python0 0
esteinig/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Language:Perl0 0
esteinig/tonic
Implements a dangerous configuration, not for general use
Language:Rust0 0
esteinig/wf-artic
ARTIC SARS-CoV-2 workflow and reporting
Language:Python0 0