John Didion

biotools. A list of useful bioinformatics resources

atropos. An NGS read trimming tool that is specific, sensitive, and speedy. (production)

pairwise-alignment. Catalogue of pairwise alignment algorithms and benchmarks

xphyle. Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)

Zooper. Zotero plugin for updating metadata and managing PDFs. (alpha)

beekeeper. A worker pool library for Rust

autoclick. Create Click-based CLIs from python3 type annotations (beta)

pest-test. Testing framework for pest parser (similar to `tree-sitter test`)

feedme. A simple, flexible, and extensible RSS and Atom parser for Ruby. Based on the popular SimpleRSS library, but with many nice extra features. (retired)

OpenBioinformaticsWorkshops. Open courseware for workshops in applied bioinformatics

papers2. Python library for interacting with a Papers2 database, plus scripts to export into various formats. (beta)

genomics_scripts. Python scripts and functions for doing things with different types of genomic data. (unsupported)

wdl-rs. Rust parser for Workflow Description Language (WDL)

driver. Generic base class for batch programs. (unsupported)

seqio. A library for high-performance reading and writing of common NGS formats. (pre-alpha)

rna-quick. Differential gene, transcript, exon, and splice junction testing framework. (pre-alpha)

tree-sitter-wdl. Tree-sitter grammar for WDL (Workflow Description Language)

labels. This is a simple program to generate labels from a table (CSV file). (production)

dxcompiler-compile-action. A GitHub action to compile a WDL workflow using dxCompiler

subby. Python subprocesses simplified.

ngsindex. Parsers for common NGS index formats (production)

ngstream. Simple reading/streaming of NGS reads from SRA. (alpha)

DEUtils. Utilities for differential expression testing. (beta)

pest-wdl. Pest parser grammar for Workflow Description Language (WDL)

jwnl. Java library for accessing WordNet. (retired)

docparse. Parse python docstrings (beta)

imetric-api. Project done during an NHGRI hackathon. (unsupported)

htsget-server. htsget server; pre-alpha, deprecated (see https://gitlab.com/genomicsengland/htsget/gel-htsget instead)

fancyplots. Some useful plots for genomic data, in base R. (beta)

hon. An opinionated Python project management tool (pre-alpha)

pytest-datadir-nng. The *next* next generation of python-datadir

wdlkit. WDL toolkit

clasp. Cell Line Authentication by SNP Profiling (CLASP). (production)

pokrok. Use any progress bar package with a simple API (production)

cwl-v1.2. Released CWL v1.2 specification

audiodrama. My audio drama feeds OPML

IndexTools. IndexTools is a toolkit for extremely fast NGS analysis based on index files.