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biotools
A list of useful bioinformatics resourcesatropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)pairwise-alignment
Catalogue of pairwise alignment algorithms and benchmarksxphyle
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)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 bioinformaticspapers2
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)seqio
A library for high-performance reading and writing of common NGS formats. (pre-alpha)driver
Generic base class for batch programs. (unsupported)ngsindex
Parsers for common NGS index formats (production)subby
Python subprocesses simplified.ngstream
Simple reading/streaming of NGS reads from SRA. (alpha)labels
This is a simple program to generate labels from a table (CSV file). (production)tree-sitter-wdl
Tree-sitter grammar for WDL (Workflow Description Language)knitrtools
Library of utilities for use in RMarkdown documents. (beta)jwnl
Java library for accessing WordNet. (retired)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)hon
An opinionated Python project management tool (pre-alpha)wdlkit
WDL toolkitpest-wdl
Pest parser grammar for Workflow Description Language (WDL)audiodrama
My audio drama feeds OPMLjdidion.github.io
dxcompiler-compile-action
A GitHub action to compile a WDL workflow using dxCompilerdocparse
Parse python docstrings (beta)fancyplots
Some useful plots for genomic data, in base R. (beta)DEUtils
Utilities for differential expression testing. (beta)clasp
Cell Line Authentication by SNP Profiling (CLASP). (production)pytest-datadir-nng
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