Michael Hall

rasusa. Randomly subsample sequencing reads or alignments

lrge. Genome size estimation from long read overlaps

ssubmit. Submit slurm sbatch jobs without a script

nohuman. Remove human reads from a sequencing run

compression_benchmark. Benchmarking FASTQ compression with 'mature' compression algorithms

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)

ontime. Extract subsets of ONT (Nanopore) reads based on time

NanoVarBench. Evaluating Nanopore-based bacterial variant calling

drprg. Drug Resistance Prediction with Reference Graphs

skc. Shared k-mer content between two genomes

taeper. A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

container_recipes. Repository with all my container recipes 👩‍🍳

tbpore. Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

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

streamformatics. Real-time species-typing visualisation for nanopore data.

fast5seek. Subset of fast5 files contained in a fastq, BAM, or SAM file.

pistis. Quality control plotting for long reads

MemoryUnits. Python objects for dealing with metric units and memory, file, and genome sizes 💾

head_to_head_pipeline. Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

reveal-hugo-nord. A nord-themed reveal-hugo presentation template

bioscripts. Collection of scripts for doing various tasks

thesis. My PhD thesis

eipp-2019-singularity. Singularity group project for EIPP 2019

MTB_masks. A collection of genome masks for Mycobacterium tuberculosis

fastq-dl. Download FASTQ files from SRA or ENA repositories.

pandora_analysis_pipeline. Python

Sepsis-methylation. Pipeline to analyse the dRNA methylation of sepsis samples.

Longitude_pipeline. Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.

Mykrobe_tb_workflow. A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

mykrobe. Antibiotic resistance prediction in minutes

envs-primer. Presentation for EBI 2021 Predocs on software environments and containers

tinysink. Synchronise Nanopore reads with a server.

unimelb-reveal-template. A University of Melbourne reveal.js theme and template

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

bioconda-recipes. Conda recipes for the bioconda channel.

bam_slice. Cut slices out of a BAM file given a list of positions.

snakefmt. The uncompromising Snakemake code formatter

syri. Synteny and Rearrangement Identifier

rust. Empowering everyone to build reliable and efficient software.