Visualise and analyse nanopore (ONT) raw signals

a tool for simulating nanopore raw signal data

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

SquiggleKit: A toolkit for manipulating nanopore signal data

A grammar of graphics for comparative genomics

Scalene: a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals

CAMISIM: Simulating metagenomes and microbial communities

PRONAME is an open-source bioinformatics pipeline that allows processing and significantly increasing the accuracy of Nanopore metabarcoding sequencing data.

gutSMASH

Toolbox for comparative genomics of MAGs

This repository focuses on the metagenomic analysis of bioaerosols using nanopore sequencing. It highlights our use of nanopore's R10 chemistry for its high accuracy and throughput, alongside the R…

GTDB => NCBI

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

From annotated genomes to metabolic screening in large scale microbiotas

A complete pipeline for metagenomic analysis

A distill blog and showcase about building distill websites and blogs!

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Multi-omics factor analysis v2

Open-source usearch

R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

A tool for semi-automatic cell type classification

MACS -- Model-based Analysis of ChIP-Seq

muon is a multimodal omics Python framework

Single-cell analysis in Python. Scales to >1M cells.

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.