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/pafpy
A lightweight library for working with PAF (Pairwise mApping Format) files
mbhall88/reveal-hugo-nord
A nord-themed reveal-hugo presentation template
mbhall88/bioscripts
Collection of scripts for doing various tasks
mbhall88/thesis
My PhD thesis
mbhall88/reveal-hugo-ebi
An EBI-themed reveal.js presentation template powered by reveal-hugo
mbhall88/Sepsis-methylation
Pipeline to analyse the dRNA methylation of sepsis samples.
mbhall88/Mykrobe_tb_workflow
A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe
mbhall88/unimelb-reveal-template
A University of Melbourne reveal.js theme and template
mbhall88/biofast
Benchmarking programming languages/implementations for common tasks in Bioinformatics
mbhall88/clap
A full featured, fast Command Line Argument Parser for Rust
mbhall88/CLI11
CLI11 is a command line parser for C++11 and beyond that provides a rich feature set with a simple and intuitive interface.
mbhall88/csi-rust
Slides for Computational Sciences Initiative (CSI) Bioinformatics Seminar on Rust
mbhall88/cyvcf2
cython + htslib == fast VCF and BCF processing
mbhall88/doherty-seminar-20210408
Slides for my seminar at the Doherty Institute on 08/04/2021
mbhall88/group-meeting-20221003
Slides for my group meeting presentation [03/10/2022]
mbhall88/homebrew-bio
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
mbhall88/just-feedstock
A conda-smithy repository for just.
mbhall88/LemurPaper
Analysis for paper about Lemur with TB
mbhall88/m6a-benchmark
mbhall88/mykrobe-data
Data for mykrobe command line tool
mbhall88/nom
Rust parser combinator framework
mbhall88/pandora_simulations
Pipeline for the simulations to evaluate de novo variant discovery in pandora
mbhall88/pbs-torque
mbhall88/predocday-20210304
Slides for my presentation at the EMBL-EBI Predoc Day on 04/03/2021
mbhall88/qmrl-slides
Slides for presentation to the Queensland Mycobacterium Reference Laboratory 24/02/2022
mbhall88/rootstock
Clone me to create your Manubot manuscript
mbhall88/statannotations
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
mbhall88/TAC3_Presentation
Slides accompanying the presentation for my third-year thesis advisory committee meeting
mbhall88/TAC3_Report
Third-year report for my EMBL-EBI Thesis Advisory Committee (TAC)
mbhall88/WHO-correspondence
Analysis pipeline for the 2021 WHO catalogue Correspondence to the Lancet Microbe