BOL

pypi.org - DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a...

Julia Programming Language – A Real Python & R Alternative

github.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...

Python projects

TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specifying a different path. Use the Terminal or an Anaconda Prompt for the...

github.com - There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise....

bioconda.github.io - Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. 

Brief Overview of Snakemake Pipeline Commands

github.com - A curated list of awesome pipeline toolkits ... https://github.com/pditommaso/awesome-pipeline

github.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...