Michael Hall's Projects
Repo to hold all my config files
Slides for my CPG (Centre for Pathogen Genomics) bioinformatics clinic on 08/04/2024.
Slides for my talk at the annual Australian Society for Microbiology conference
A tool for removing redundant genomes from a set of assemblies
Cut slices out of a BAM file given a list of positions.
Pipeline to basecall the TB sputum nanopore data
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Conda recipes for the bioconda channel.
Utilities for building and managing bioconda recipes
Benchmarking programming languages/implementations for common tasks in Bioinformatics
Collection of scripts for doing various tasks
A full featured, fast Command Line Argument Parser for Rust
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
CLI11 is a command line parser for C++11 and beyond that provides a rich feature set with a simple and intuitive interface.
Benchmarking FASTQ compression with 'mature' compression algorithms
Calculate confidence scores from Kraken2 output
Repository with all my container recipes 👩🍳
A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
Slides for Computational Sciences Initiative (CSI) Bioinformatics Seminar on Rust
Color Universal Design colourblind-friendly python matplotlib palette
cython + htslib == fast VCF and BCF processing
Slides for my seminar at the Doherty Institute on 08/04/2021
Drug Resistance Prediction with Reference Graphs
Repository of prebuilt indices for Dr. PRG
Workflow and files associated with the paper for DrPRG
Workflow for analysing Nanopore amplicon data for the Dunstan group
Singularity group project for EIPP 2019
Presentation for EBI 2021 Predocs on software environments and containers
Subset of fast5 files contained in a fastq, BAM, or SAM file.
Python3 scripts to manipulate FASTA and FASTQ files