mbhall88

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University of Melbourne | Doherty Institute

Sunshine Coast, Australia

Organizations

iqbal-lab-org

Mykrobe-tools

rust-bio

snakemake

Snakemake-Profiles

Michael Hall's repositories

rasusa

Randomly subsample sequencing reads or alignments

Language:RustMIT212 6 39

ssubmit

Submit slurm sbatch jobs without a script

Language:RustUnlicense65 2 4

compression_benchmark

Benchmarking FASTQ compression with 'mature' compression algorithms

Language:PythonMIT31 1 5

nohuman

Remove human reads from a sequencing run

Language:RustMIT24 1 1

psdm

Compute a pairwise SNP distance matrix from one or two alignment(s)

Language:RustMIT22 3 2

ontime

Extract subsets of ONT (Nanopore) reads based on time

Language:RustMIT20 1 5

container_recipes

Repository with all my container recipes 👩‍🍳

Language:DockerfileMIT15 2 1

NanoVarBench

Evaluating Nanopore-based bacterial variant calling

Language:PythonMIT15 5 5

classification_benchmark

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification

Language:PythonMIT11 20

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Language:PythonMIT11 6 43

pistis

Quality control plotting for long reads

Language:PythonMIT10 3 2

cud

Color Universal Design colourblind-friendly python matplotlib palette

Language:PythonUnlicense2 10

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonMIT2 10

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellMIT1 10

rust

Empowering everyone to build reliable and efficient software.

Language:RustNOASSERTION1 10

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

Language:RustMIT100

snakefmt

The uncompromising Snakemake code formatter

Language:PythonMIT1 10

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

Language:HTMLMIT1 10

.dotfiles

Repo to hold all my config files

Language:Shell020

20240408-CPG-clinic

Slides for my CPG (Centre for Pathogen Genomics) bioinformatics clinic on 08/04/2024.

Language:JavaScriptMIT010

20240704-ASM-slides

Slides for my talk at the annual Australian Society for Microbiology conference

Language:JavaScriptMIT000

bioconda-utils

Utilities for building and managing bioconda recipes

Language:PythonMIT000

bioconda.github.io

Bioconda is a distribution of bioinformatics software realized as a channel for the versatile package manager Conda.

Language:HTML000

cf-scripts

Flagship repo for cf-regro-autotick-bot

Language:PythonNOASSERTION000

noodles

Bioinformatics I/O libraries in Rust

Language:RustMIT000

notes

My notes for tips and tricks

000

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.

Language:CythonMIT000

rust-script-feedstock

A conda-smithy repository for rust-script.

BSD-3-Clause000

ssubmit-feedstock

A conda-smithy repository for ssubmit.

BSD-3-Clause000

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

Language:PythonBSD-3-Clause010