Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

The Leek group guide to data sharing

Track fitness of deletion mutants with a randomly barcoded random insertion library

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

Python Data Science Handbook: full text in Jupyter Notebooks

Clean APIs for data cleaning. Python implementation of R package Janitor

Source Code for 'Thinking in Pandas' by Hannah Stepanek

Effective Python: Second Edition — Source Code and Errata for the Book

✂️ ⚡ Rapid haploid variant calling and core genome alignment

ARTIC nanopore protocol for nCoV2019 novel coronavirus

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Prediction of prophages from bacterial genomes

SARS-CoV-2 parallel sequencing by Illumina and Oxford Nanopore Technologies

Pipelines for assembling NGS data from Seattle flu study.

Plotting scripts for long read sequencing data

Very fast ONT basecaller

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

Plotting tools for nanopore methylation data

Detecting methylation using signal-level features from Nanopore sequencing reads

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

Notes from Raymond Hettinger's talk at PyCon US 2013.