mbhall88

User data from Github https://github.com/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:RustMIT218 6 40

ssubmit

Submit slurm sbatch jobs without a script

Language:RustUnlicense65 2 4

lrge

Genome size estimation from long read overlaps

Language:RustMIT4300

nohuman

Remove human reads from a sequencing run

Language:RustMIT34 1 1

compression_benchmark

Benchmarking FASTQ compression with 'mature' compression algorithms

Language:PythonMIT32 1 5

psdm

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

Language:RustMIT24 3 2

ontime

Extract subsets of ONT (Nanopore) reads based on time

Language:RustMIT21 1 5

container_recipes

Repository with all my container recipes 👩‍🍳

Language:DockerfileMIT15 2 1

NanoVarBench

Evaluating Nanopore-based bacterial variant calling

Language:PythonMIT15 4 5

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

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

20241205-uqccr-symposium

Slides for my presentation at the 2024 UQCCR Infectious Diseases Theme Showcase

Language:JavaScriptMIT000

AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

Language:PythonMIT000

bioconda-docs

Documentation for bioconda

Language:SCSSMIT000

bioconda-utils

Utilities for building and managing bioconda recipes

Language:PythonMIT010

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

minimap2-rs

Rust bindings to minimap2 library

Language:RustNOASSERTION000

needletail

Fast FASTX parsing and k-mer methods in Rust

Language:RustMIT000

noodles

Bioinformatics I/O libraries in Rust

Language:RustMIT000

notes

My notes for tips and tricks

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open-data-registry

A registry of publicly available datasets on AWS

Language:PythonApache-2.0000

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

statannotations-feedstock

A conda-smithy repository for statannotations.

BSD-3-Clause000