Michael Hall (@mbhall88)
github

mbhall88

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Top repositories

1

rasusa

Randomly subsample sequencing reads or alignments
Rust
203
star
2

ssubmit

Submit slurm sbatch jobs without a script
Rust
62
star
3

pafpy

A lightweight library for working with PAF (Pairwise mApping Format) files
Python
31
star
4

compression_benchmark

Benchmarking FASTQ compression with 'mature' compression algorithms
Python
30
star
5

taeper

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.
Python
19
star
6

drprg

Drug Resistance Prediction with Reference Graphs
Rust
19
star
7

nohuman

Remove human reads from a sequencing run
Rust
19
star
8

ontime

Extract subsets of ONT (Nanopore) reads based on time
Rust
19
star
9

skc

Shared k-mer content between two genomes
Rust
17
star
10

psdm

Compute a pairwise SNP distance matrix from one or two alignment(s)
Rust
17
star
11

container_recipes

Repository with all my container recipes 👩‍🍳
Dockerfile
15
star
12

NanoVarBench

Evaluating Nanopore-based bacterial variant calling
Python
14
star
13

streamformatics

Real-time species-typing visualisation for nanopore data.
JavaScript
13
star
14

fast5seek

Subset of fast5 files contained in a fastq, BAM, or SAM file.
Python
11
star
15

tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
Python
11
star
16

pistis

Quality control plotting for long reads
Python
10
star
17

classification_benchmark

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification
Python
9
star
18

MemoryUnits

Python objects for dealing with metric units and memory, file, and genome sizes 💾
Python
7
star
19

reveal-hugo-nord

A nord-themed reveal-hugo presentation template
CSS
6
star
20

bioscripts

Collection of scripts for doing various tasks
Python
5
star
21

head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
Jupyter Notebook
5
star
22

thesis

My PhD thesis
Jupyter Notebook
4
star
23

rawmeth

Package for exploring raw signal of nanopore reads that have been resquiggled with nanoraw.
Python
4
star
24

eipp-2019-singularity

Singularity group project for EIPP 2019
Jupyter Notebook
3
star
25

reveal-hugo-ebi

An EBI-themed reveal.js presentation template powered by reveal-hugo
CSS
2
star
26

Longitude_pipeline

Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.
Python
2
star
27

Sepsis-methylation

Pipeline to analyse the dRNA methylation of sepsis samples.
Jupyter Notebook
2
star
28

MTB_masks

A collection of genome masks for Mycobacterium tuberculosis
2
star
29

pandora_analysis_pipeline

Python
2
star
30

cud

Color Universal Design colourblind-friendly python matplotlib palette
Python
2
star
31

tubemaps_pilot

Playing around with getting sequence tubemaps to work for population reference graphs.
xBase
1
star
32

envs-primer

Presentation for EBI 2021 Predocs on software environments and containers
JavaScript
1
star
33

tinysink

Synchronise Nanopore reads with a server.
Shell
1
star
34

bam_slice

Cut slices out of a BAM file given a list of positions.
Python
1
star