UriNeri

funannotate. Eukaryotic Genome Annotation Pipeline

pyodide-recipes. Collections of package recipes for Pyodide

EVscope. EVscope: A Modular Pipeline for EV-Enriched Total RNA-seq QC, EM-Weighted Coverage Profiling, and RNA-Biotype Annotation

rasusa. Randomly subsample sequencing reads or alignments

fastars. Fast random access sequence retrieval from fasta files

FastDedup. A fast and memory-efficient FASTX PCR deduplication tool.

floria. Strain-level haplotyping for metagenomes with short or long-reads.

bwa-mem2. The next version of bwa-mem

rnapkin. drawing RNA secondary structure with style; instantly

genotypst. genotypst: A bioinformatics Typst package for bioinformatics data analysis and visualization

barbell. Extremely fast and accurate Nanopore demultiplexing

metaMDBG. MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

iphop. Python

oxford-bioinformatics-template. Improved version of the Oxford Bioinformatics paper template

mobile. Lichess mobile app

Iterative-blast-v.1.0. The program and codes iterative blast

mininear. A NumPy port of the NEAR code for embedding protein sequences.

rolypolious. RNA virus analysis toolkit

veryfasttree. Efficient phylogenetic tree inference for massive taxonomic datasets

phlegm. Phage Homomer Level Estimator and Generator Method

FamDB. FamDB file format library and utilities

paraseq. A minimal copy fastq and fasta reader built for parallel support and paired end processing

Biochef. BioChef a tool for fast browser tests in genome and proteome.

just. 🤖 Just a command runner

hoodini-colab. Google Colab notebook for running Hoodini gene neighborhood analysis with a nice GUI

arkadia. Ndarray backed KD-tree that is more suitable for data science use cases

B-PPI. B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction

learnMSA. Learning and Aligning Large Protein Families with support of protein language models.

veryfasttree-python. VeryFastTree Python Bindings

local-cd-search. Protein annotation using local PSSM databases from CDD

orphos. Fast, parallel Rust implementation of Prodigal for prokaryotic gene prediction in microbial genomes

detectADAM. Mining publicly available sequencing datasets for viral information

spaed. Segmentation of phage endolysin domains

PropagAtE. Prophage Activity Estimator

polars-expr-hopper. A Polars plugin providing a 'hopper' of expressions for automatic, schema-aware application.

abyss. :microscope: Assemble large genomes using short reads

FCSeqTools.jl. eaDCA and Sequence Tools

phylotree-rs. Rust crate to deal with phylogenetic trees

bigtree. Tree Implementation and Methods for Python, integrated with list, dictionary, pandas and polars DataFrame.

boltz. Official repository for the Boltz biomolecular interaction models

pyrodigal-rv. A Pyrodigal extension to predict genes in RNA viruses.

prfect. Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes

binchicken. Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly

CherryML. Scalable Maximum Likelihood Estimation of Phylogenetic Models

parasail. Pairwise Sequence Alignment Library

parasail-python. Python bindings for the parasail C library.

domainator. A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.

TRILL. Sandbox for Deep-Learning based Computational Protein Design

palmsite. PalmSite — RdRP catalytic center predictor.

LCCScore. Python

polarify. Simplifying conditional Polars Expressions with Python 🐍 🐻‍❄️

paper-to-audio. Convert documents into audio with LLMs

spacer_bench. Jupyter Notebook

gpn. Genomic Pre-trained Network

pyfastx. a python package for fast random access to sequences from plain and gzipped FASTA/Q files

polars-bio-workshop. Jupyter Notebook

plasmid_network. React + Cosmograph visualization tool for exploring antiphage defense systems in plasmids from Payne, Mestre, Zheng et al 2026

pysylph. PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.

BBTools. BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.

EsViritu. Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

SillyTavern. LLM Frontend for Power Users.

sparql-llm. 🦜✨ Chat system, MCP server, and reusable components to improve LLMs capabilities when generating SPARQL queries

awesome-rna-virus-tools. An community curated awesome list of tools, software, databases and other resources for working/analysing RNA Viruses

polars_list_utils. Polars Plugin for List-type Columns

polars-utils. Python

grape. 🍇 GRAPE is a Rust/Python Graph Representation Learning library for Predictions and Evaluations

fast_gliner. Python bindings to Inference engine for GLiNER models written in Rust

trrex. Efficient string matching with regular expressions

GLiREL. Generalist and Lightweight Model for Relation Extraction (Extract any relationship types from text)

elfen. A python package to efficiently extract linguistic features for text/NLP datasets

cogent3. Comparative Genomics Toolkit 3

pyranges1. Pyranges: a Python framework for ultrafast sequence interval operations

viralquest. A user-friendly pipeline for viral diversity analysis and characterization.

pubmed_parser. :clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

ty-vscode. A Visual Studio Code extension for ty.

metapub. Python toolkit for NCBI metadata (via eutils) and pubmed article text mining -- official primary repo.

SARS-CoV-2_genome_structure. PostScript

rouls. Rouskin Lab Tools

encat-spec-and-tools. protocol spec and tools

data-gov-il-mcp. Advanced MCP server for seamless access to Israeli Government Open Data

sassy. Fast approximate string searching

deacon. Fast DNA search and [host] depletion using minimizers

pyaragorn. Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

butterfish. A shell with AI superpowers

RNAsselem. a Python package for descriptive analysis of RNA secondary structure elements in viral genomes

genopype. Architecture for creating bash pipelines, in particular, for bioinformatics

tree-sitter. An incremental parsing system for programming tools

gffcompare. classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

plate. Rich-text editor with AI and shadcn/ui

rolypoly. RNA virus analysis toolkit

RooFlow. RooFlow - Enhanced Memory Bank System with ☢️Footgun Power☢️ Next-gen Memory Bank system with five integrated modes and system-level customization. Uses Roo Code's experimental "Footgun" feature for deep AI assistant customization while maintaining efficient token usage!

omnifluss. Computational workflow for virus genome reconstruction

snakevir. Python

plot_phylo. Python package to plot a phylogenetic tree on an existing matplotlib axis.

suvtk. Tool to submit viral sequences to Genbank.

globalspacers_scripts. Scripts used in the global spacer project

paper-search-mcp. MCP, CLI, Skills for searching and downloading academic papers from multiple sources like arXiv, PubMed, bioRxiv, etc.

FastAAI. Python

cmap. Scientific colormaps for python, with only numpy dependency

dspy. DSPy: The framework for programming—not prompting—language models