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

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

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. [Manuscript preprint] (https://www.biorxiv.org/content/10.1101/2024.07.08.602471v1)

trackcluster -[Python] - trackcluster is an isoform calling and quantification pipeline for long RNA/cDNA reads. Published in Genome Research, 2020

mitovar -[Python] - mitovar is a pipeline used for mtDNA genome assembly from NGS reads. Published in DNA Research, 2018

primerdiffer -[Python] - 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.
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