Software

Hammerhead - [Python] - Hammerhead is a pipeline for the detection of bacterial DNA modifications and fix modification induced assembly error from Nanopore R10.4.1 reads. Published in Genome Research, 2024
nanoSundial - [Python] - nanoSundial is a python command line tool to facilitate the de novo finding of DNA/RNA modification sites by signal compare. Published in Cell reports methods, 2025
nanoCEM -[Python] - The nanopore current events magnifier (nanoCEM) is a python command line to facilitate the analysis of DNA/RNA modification sites by visualizing statistical features of current events. Published in NARGAB, 2024

2. RNA splicing and isoform analysis tools Link to heading

trackcluster -[Python] - trackcluster is an isoform calling and quantification pipeline for long RNA/cDNA reads. Published in Genome Research, 2020
trackcluster-rs [Rust] -trackcluster-rs is a rust re-write of trackcluster with the same algorithm but faster processing for large dataset.
trackclusterTU [Rust] - trackclusterTU is a fast interval similarity and scalable clustering for bacterial transcript units (TUs) from mapped long reads.

Giraffe - [Python] - Giraffe is used for long read QC, can be used to calculate and visualize basic statistics for nanopore/pacbio long reads, including observed/estimated read quality; gc bias for reads; homopolymer accuracy and others.Published in CSBJ 2024 Some of these features has been used in our benchmarking papers on single cell DNA sequencing and DNA methylation profiling.
ANASFV - [Python] - ANASFV is a pipeline used for the analysis of african swine fever virus. Published in Microbial Genomics, 2025
primerdiffer -[Python & C] - primerdiffer is a pipeline used to design primers in a large batch. Published in Bioinformatics, 2023
- primervcf - [Python] - primervcf is a sub-module for primerdiffer, to design haplotyping primers using vcf file.
mitovar -[Python] - mitovar is a pipeline used for mtDNA genome assembly from NGS reads. Published in DNA Research, 2018