mbhall88
Postdoc @ University of Melbourne with @lachlancoin. Bioinformatics | Nanopore | Microbial Genomics | Software Dev.
University of Melbourne | Doherty InstituteSunshine Coast, Australia
Pinned Repositories
compression_benchmark
Benchmarking FASTQ compression with 'mature' compression algorithms
drprg
Drug Resistance Prediction with Reference Graphs
lrge
Genome size estimation from long read overlaps
nohuman
Remove human reads from a sequencing run
ontime
Extract subsets of ONT (Nanopore) reads based on time
pafpy
A lightweight library for working with PAF (Pairwise mApping Format) files
psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
rasusa
Randomly subsample sequencing reads or alignments
ssubmit
Submit slurm sbatch jobs without a script
snakefmt
The uncompromising Snakemake code formatter
mbhall88's Repositories
mbhall88/rasusa
Randomly subsample sequencing reads or alignments
mbhall88/ssubmit
Submit slurm sbatch jobs without a script
mbhall88/lrge
Genome size estimation from long read overlaps
mbhall88/nohuman
Remove human reads from a sequencing run
mbhall88/compression_benchmark
Benchmarking FASTQ compression with 'mature' compression algorithms
mbhall88/psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
mbhall88/ontime
Extract subsets of ONT (Nanopore) reads based on time
mbhall88/container_recipes
Repository with all my container recipes 👩🍳
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
mbhall88/fastq-dl
Download FASTQ files from SRA or ENA repositories.
mbhall88/bioconda-recipes
Conda recipes for the bioconda channel.
mbhall88/rust
Empowering everyone to build reliable and efficient software.
mbhall88/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
mbhall88/.dotfiles
Repo to hold all my config files
mbhall88/20241205-uqccr-symposium
Slides for my presentation at the 2024 UQCCR Infectious Diseases Theme Showcase
mbhall88/AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
mbhall88/bioconda-docs
Documentation for bioconda
mbhall88/bioconda-utils
Utilities for building and managing bioconda recipes
mbhall88/bioconda.github.io
Bioconda is a distribution of bioinformatics software realized as a channel for the versatile package manager Conda.
mbhall88/cf-scripts
Flagship repo for cf-regro-autotick-bot
mbhall88/minimap2-rs
Rust bindings to minimap2 library
mbhall88/needletail
Fast FASTX parsing and k-mer methods in Rust
mbhall88/noodles
Bioinformatics I/O libraries in Rust
mbhall88/notes
My notes for tips and tricks
mbhall88/open-data-registry
A registry of publicly available datasets on AWS
mbhall88/pysam
Pysam 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 samtools, bcftools, and tabix.
mbhall88/rust-script-feedstock
A conda-smithy repository for rust-script.
mbhall88/ssubmit-feedstock
A conda-smithy repository for ssubmit.
mbhall88/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
mbhall88/statannotations-feedstock
A conda-smithy repository for statannotations.