Fast and accurate de novo assembler for long reads

PEPPER-Margin-DeepVariant

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

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

Long read production pipelines

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

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

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

A fast tool for hybrid genome assembly of long and short reads

Yet Another Chimeric Read Detector

⛓ Long Interval Nucleotide K-mer Scaffolder

Long-reads Gap-free Chromosome-scale Assembler

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Scalable long read self-correction and assembly polishing with multiple sequence alignment

ClairS - a deep-learning method for long-read somatic small variant calling

Close assembly gaps using long-reads at high accuracy.

SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.o…

A versatile compressor of third generation sequencing reads.