Graph-based assembly phasing

SARS-CoV-2 workflow for nanopore sequence data

🔬 Genotyping tool for genome-edited samples, utilizing nanopore sequencer target sequencing

Real-Time Nanopore Analysis Pipeline: Repository for developing a real-time Nanopore sequencing pipeline to enhance cancer vaccine research. Features include real-time monitoring, sequencing endpoints, and comparative TCR analysis between Singleron and Nanopore technologies.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Snakemake pipeline to analyze retrotransposable element 'omics data.

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

Automated data mangement for Oxford Nanopore DNA sequencing instruments

Quality control plotting for long reads

Assembly and binning of metagenomes

Nanomotif - a tool for identifying methylated motifs in metagenomic samples

Scripts and data regarding Vampyrellida genomics.

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

Assembly and intrahost/low-frequency variant calling for viral samples

Oxford Nanopore's Basecaller

Basic workflow for nanopore sequencing data

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Structural variation caller using third generation sequencing