Tools for high-throughput sequencing data

An R toolkit for single cell genomics

Trimming illumina paired-end and single ended data

Signal-level algorithms for MinION data

A tool for aligning sequencing reads to reference

Burrow-Wheeler Aligner for short-read alignment

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenome

Finding and removing adapters from Nanopore reads

Research release basecalling models and configurations

A PyTorch Basecaller for Oxford Nanopore Reads

Galaxy is a use-friendly web interface to a lot of bioinformatics tools. It is very popular for analyzing NGS data.