simple web-based, free and open-source visual novel editor that can be used in a web browser. It is written in JavaScript without using any third party libraries and thus does not require additional software installation. The engine uses standard HTML document elements such as div and img.

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

SALSA: A tool to scaffold long read assemblies with Hi-C data

Toolkit for calling structural variants using short or long reads

A Python library to visualize and analyze long-read transcriptomes

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

Fast and space-efficient taxonomic classification of long reads

Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

Suite of tools for use in genome assembly and consensus. Work in progress.

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Extract methylation calls from long reads (ONT/ PacBio)

Merge transcriptome read-to-genome alignments into non-redundant transcript models

Analyse RNA feature distributions.

Minor Variant Calling and Phasing Tools

Longread PacBio sequencing processing for WGS and PureTarget

HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).

longcallR_nn is a variant caller specifically designed for long-read RNA-seq data, utilizing a ResNet50 model.

A lightweight wrapper to run minimap2 (v2.30) alignments directly on BAM file

Long read structural variants in rare disease cohort

tool for long read transcriptome assembly

Long-read RNA-seq nextflow pipeline for quantification, novel isoform discovery and quality control

Performs archiving and transfer of Nanopore sequencing data

comprehensive reproducible benchmarking framework for single-cell and spatial long-read transcriptomics

preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

SIMulator for Long read transcriptome Analysis with RNA DecaY model

Shallow Nanopore Sequencing for Transcriptomics

MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing

Analyses of Penter, Borji & Nagler et al., Nature Communications 2024