mbhall88 Goto Github PK

group-meeting-20221003

Slides for my group meeting presentation [03/10/2022]

head_to_head_pipeline

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

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

journal-club-20200803

Journal club presentation for https://advances.sciencemag.org/content/6/22/eaba4901

just-feedstock

A conda-smithy repository for just.

keep-a-changelog

If you build software, keep a changelog.

kraken2

The second version of the Kraken taxonomic sequence classification system

lemurpaper

Analysis for paper about Lemur with TB

longitude_pipeline

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

lsf

Cookiecutter for snakemake LSF profile

m6a-benchmark

make_prg

Code to create a PRG from a Multiple Sequence Alignment file

masters_project

mbhall88.github.io

The code behind my personal blog. Originally a fork of https://github.com/hydecorp/hydejack-starter-kit

memoryunits

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

mtb_masks

A collection of genome masks for Mycobacterium tuberculosis

mykrobe

Antibiotic resistance prediction in minutes

mykrobe-data

Data for mykrobe command line tool

mykrobe_tb_workflow

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

nanosim-h

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

nohuman

Remove human reads from a sequencing run

nom

Rust parser combinator framework

ontime

Extract subsets of ONT (Nanopore) reads based on time

pafpy

A lightweight library for working with PAF (Pairwise mApping Format) files

pandora

Pan-genome inference with long error-prone sequencing reads

pandora_analysis_pipeline

pandora_simulations

Pipeline for the simulations to evaluate de novo variant discovery in pandora

pbs-torque

pggb

the pangenome graph builder

pistis

Quality control plotting for long reads