A Snakemake workflow based on the official short tutorial: https://snakemake.readthedocs.io/en/v7.32.3/tutorial/short.html

🍄 Qiime2 ITS classifiers for the UNITE database

A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT

a pipeline to build similarity maps of protein space

Resolve production issues, fast. An open source observability platform unifying session replays, logs, metrics, traces and errors powered by Clickhouse and OpenTelemetry.

A realtime CRDT-based document store, backed by S3.

Sobolev alignment of deep probabilistic models for comparing single cell profiles

A single molecule sequence assembler for genomes large and small.

Ultra-fast and memory-efficient (meta-)genome assembler

A fast and sensitive gapped read aligner

A real-time data backend for browser-based applications.

Ukama hardware stuff

Ukama's open-source cellular network

A data framework for biology.

A distributed system for running WebSocket services at scale.

Code for the paper Hybrid Spectrogram and Waveform Source Separation

Containers for machine learning

A curated list of resources for Image and Video Deblurring

Light-weight Jupyter notebook tracker.

Run Python functions locally or in the cloud. Built for computational science.

A latent text-to-image diffusion model

This notebook takes one 16S sample from an Illumina MiSeq run, runs it through Kraken 2 on Toolchest, and plots a rough sketch of the microbial composition of the sample.

A monorepo for Jamsocket client libraries, the CLI, and examples

Scaffold for setting up a hosted jupyter notebook on the Jamsocket platform

Toolchest Python client

R Client for Toolchest

This repo collects the list of conferences/meetings/workshops etc. related to microbiome science and tools.

The second version of the Kraken taxonomic sequence classification system

hybrid assembly pipeline for bacterial genomes