jdidion

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)

pest-test

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

wdl-rs

Rust parser for Workflow Description Language (WDL)

subby

Python subprocesses simplified.

cwl-v1.2

Released CWL v1.2 specification

jdidion.github.io

pest-wdl

Pest parser grammar for Workflow Description Language (WDL)

pytest-datadir-nng

The *next* next generation of python-datadir

tree-sitter-wdl

Tree-sitter grammar for WDL (Workflow Description Language)

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

cachier

Persistent, stale-free, local and cross-machine caching for Python functions.

career-ladder

Framework for creating career ladders

FuBAR

Fun with Bioinformatics Algorithms in Rust

IndexTools

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

InstantTee

Rust implementation of the tee command using splice() and tee() Linux system calls. It is 4-5 times faster than GNU.

jd-test-repo

A test repo

leviosam2

Fast and accurate coordinate conversion between assemblies

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

read-structure

release-plz

Publish Rust crates from CI with a Release PR.

seq_geom_parser

Testing out rust parsing of single-cell library geometry specifications

streammd

Single-pass probabilistic duplicate marking of alignments with a Bloom filter.

syncmers

Library for finding syncmers from &[u8] in rust

testing-proc-macros

Example of structuring a proc macro crate for testability

tree-sitter

An incremental parsing system for programming tools

tree-sitter-python

Python grammar for tree-sitter

wdlTools

WDL tools for parsing, type-checking, and more