mbhall88/pistis

This repository has been archived on 14/May/2024
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Python
License
MIT License
Created over 6 years ago
Updated 4 months ago

mbhall88/pistis

mbhall88

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Quality control plotting for long reads

rasusa

Randomly subsample sequencing reads or alignments

ssubmit

Submit slurm sbatch jobs without a script

pafpy

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

compression_benchmark

Benchmarking FASTQ compression with 'mature' compression algorithms

taeper

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

drprg

Drug Resistance Prediction with Reference Graphs

nohuman

Remove human reads from a sequencing run

ontime

Extract subsets of ONT (Nanopore) reads based on time

skc

Shared k-mer content between two genomes

psdm

Compute a pairwise SNP distance matrix from one or two alignment(s)

container_recipes

Repository with all my container recipes 👩‍🍳

streamformatics

Real-time species-typing visualisation for nanopore data.

NanoVarBench

Evaluating Nanopore-based bacterial variant calling

fast5seek

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

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

MemoryUnits

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

reveal-hugo-nord

A nord-themed reveal-hugo presentation template

bioscripts

Collection of scripts for doing various tasks

head_to_head_pipeline

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

Jupyter Notebook

thesis

Jupyter Notebook

rawmeth

Package for exploring raw signal of nanopore reads that have been resquiggled with nanoraw.

eipp-2019-singularity

Singularity group project for EIPP 2019

Jupyter Notebook

reveal-hugo-ebi

An EBI-themed reveal.js presentation template powered by reveal-hugo

Longitude_pipeline

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

Sepsis-methylation

Pipeline to analyse the dRNA methylation of sepsis samples.

Jupyter Notebook

MTB_masks

A collection of genome masks for Mycobacterium tuberculosis

pandora_analysis_pipeline

cud

Color Universal Design colourblind-friendly python matplotlib palette

tubemaps_pilot

Playing around with getting sequence tubemaps to work for population reference graphs.

envs-primer

Presentation for EBI 2021 Predocs on software environments and containers

tinysink

Synchronise Nanopore reads with a server.

bam_slice

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