HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

The Flexible Demultiplexer

Nanopore RNASeq data

Visualise and analyse nanopore (ONT) raw signals

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

The buttery eel - a slow5 guppy/dorado basecaller wrapper

Reference-guided transcript discovery and quantification for long read RNA-Seq data

A NextFlow pipeline for m6A detection from Nanopore direct RNA-seq data

A curated list of awesome nanopore analysis tools.

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Alternative Promoter Analysis Packages

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

A repository to host materials needed for workship in Multiple Instance Learning

minimal example implementations for bioinformatics workflow managers

A tool to identify, orient, trim and rescue full length cDNA reads

Chunkwise Text-file Processing for 'dplyr'

deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads

Detection of m6A from direct RNA-Seq data

Tools to process and analyze deep sequencing data.

Bioconductor cheat sheet

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Contribute Packages to Bioconductor

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

OPERA-MS - Hybrid Metagenomic Assembler

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Identification of differential RNA modifications from nanopore direct RNA sequencing

Nanopore demultiplexing, QC and alignment pipeline

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.