mbhall88

rasusa

Randomly subsample sequencing reads

ssubmit

Submit slurm sbatch jobs without the need to create a script

compression_benchmark

Benchmarking fastq compression with generic (mature) compression algorithms

drprg

Drug Resistance Prediction with Reference Graphs

ontime

Extract subsets of ONT (Nanopore) reads based on time

container_recipes

Repository with all my container recipes 👩‍🍳

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

pistis

Quality control plotting for long reads

classification_benchmark

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

nohuman

Remove human reads from a sequencing run

MemoryUnits

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

NanoVarBench

Evaluating Nanopore-based bacterial variant calling

cud

Color Universal Design colourblind-friendly python matplotlib palette

bioconda-recipes

Conda recipes for the bioconda channel.

rust-htslib

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

snakefmt

The uncompromising Snakemake code formatter

snakemake

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

syri

Synteny and Rearrangement Identifier

.dotfiles

Repo to hold all my config files

20240408-CPG-clinic

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

Conifer

Calculate confidence scores from Kraken2 output

cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

drprg-paper

Workflow and files associated with the paper for DrPRG

Dunstan_nanopore_amplicon

Workflow for analysing Nanopore amplicon data for the Dunstan group

fixchr

pggb

the pangenome graph builder

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.

slurm

Cookiecutter for snakemake slurm profile

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

varifier

Variant call verification