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
Language:Python31 1 54
drprg
Drug Resistance Prediction with Reference Graphs
Language:Rust19 8 241
lrge
Genome size estimation from long read overlaps
Language:Rust430
nohuman
Remove human reads from a sequencing run
Language:Rust33 1 13
ontime
Extract subsets of ONT (Nanopore) reads based on time
Language:Rust20 1 51
pafpy
A lightweight library for working with PAF (Pairwise mApping Format) files
Language:Python31 3 53
psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
Language:Rust24 3 21
rasusa
Randomly subsample sequencing reads or alignments
Language:Rust216 6 4017
ssubmit
Submit slurm sbatch jobs without a script
Language:Rust65 2 45
snakefmt
The uncompromising Snakemake code formatter
Language:Python154 7 12629

mbhall88's Repositories

mbhall88/taeper
A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.
Language:Python19 4 20
mbhall88/eipp-2019-singularity
Singularity group project for EIPP 2019
Language:Jupyter Notebook3 2 42
mbhall88/Longitude_pipeline
Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.
Language:Python2 3 0
mbhall88/pandora_analysis_pipeline
Language:Python2 3 7
mbhall88/bam_slice
Cut slices out of a BAM file given a list of positions.
Language:Python1
mbhall88/tinysink
Synchronise Nanopore reads with a server.
Language:Shell1 2 11
mbhall88/Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
Language:Python1 0
mbhall88/keep-a-changelog
If you build software, keep a changelog.
Language:HTML1 0
mbhall88/kraken2
The second version of the Kraken taxonomic sequence classification system
Language:C++1 0
mbhall88/masters_project
Language:JavaScript4 34
mbhall88/NanoSim-H
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
Language:Python1 0
mbhall88/predoc-lunch-sem-20200311
Slides for presentation at the EBI predoc lunch seminar 11/03/2020
Language:CSS
mbhall88/predocday-20200331
Slides for my presentation at EBI Predoc Day 2020
Language:Jupyter Notebook2 0
mbhall88/reveal_presentations
Repository to host all my reveal.js presentations
Language:HTML
mbhall88/seequence
Visualisation tool for sequence alignment
Language:JavaScript2 01
mbhall88/TAC2-Presentation
Slides for the presentation of my second-year report to my thesis advisory committee
Language:CSS2 0
mbhall88/taiyaki
Training models for basecalling Oxford Nanopore reads
Language:Python1 0