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University of Melbourne | Doherty Institute
- Sunshine Coast, Australia
- https://mbh.sh
- https://orcid.org/0000-0003-3683-6208
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20240704-ASM-slides Public
Slides for my talk at the annual Australian Society for Microbiology conference
JavaScript MIT License UpdatedJul 9, 2024 -
compression_benchmark Public
Benchmarking FASTQ compression with 'mature' compression algorithms
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tldr Public
Forked from tldr-pages/tldr📚 Collaborative cheatsheets for console commands
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psdm Public
Compute a pairwise SNP distance matrix from one or two alignment(s)
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tbpore Public
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
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NanoVarBench Public
Evaluating Nanopore-based bacterial variant calling
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snakefmt Public
Forked from snakemake/snakefmtThe uncompromising Snakemake code formatter
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pistis Public archive
Quality control plotting for long reads
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rasusa Public
Randomly subsample sequencing reads or alignments
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rust-htslib Public
Forked from rust-bio/rust-htslibThis library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
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classification_benchmark Public
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
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nohuman Public
Remove human reads from a sequencing run
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20240408-CPG-clinic Public
Slides for my CPG (Centre for Pathogen Genomics) bioinformatics clinic on 08/04/2024.
JavaScript MIT License UpdatedMar 26, 2024 -
cud Public
Color Universal Design colourblind-friendly python matplotlib palette
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MemoryUnits Public
Python objects for dealing with metric units and memory, file, and genome sizes 💾
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drprg-paper Public
Workflow and files associated with the paper for DrPRG
Jupyter Notebook UpdatedFeb 28, 2024 -
ontime Public
Extract subsets of ONT (Nanopore) reads based on time
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container_recipes Public
Repository with all my container recipes 👩🍳
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ssubmit Public
Submit slurm sbatch jobs without a script
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varifier Public
Forked from iqbal-lab-org/varifierVariant call verification
Python MIT License UpdatedJan 18, 2024 -
syri Public
Forked from schneebergerlab/syriSynteny and Rearrangement Identifier
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pysam Public
Forked from pysam-developers/pysamPysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
Cython MIT License UpdatedJan 11, 2024 -
bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
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cramino Public
Forked from wdecoster/craminoA *fast* tool for BAM/CRAM quality evaluation, intended for long reads
Rust MIT License UpdatedJan 4, 2024 -
snakemake Public
Forked from snakemake/snakemakeThis is the development home of the workflow management system Snakemake. For general information, see
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Conifer Public
Forked from Ivarz/ConiferCalculate confidence scores from Kraken2 output
C BSD 2-Clause "Simplified" License UpdatedDec 20, 2023 -
Dunstan_nanopore_amplicon Public
Workflow for analysing Nanopore amplicon data for the Dunstan group
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snippy Public
Forked from tseemann/snippy✂️ ⚡ Rapid haploid variant calling and core genome alignment
Perl GNU General Public License v2.0 UpdatedOct 18, 2023