Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Structural variation caller using third generation sequencing

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Fast and accurate de novo assembler for long reads

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Long read / genome alignment software

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

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

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

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

Technology agnostic long read analysis pipeline for transcriptomes

Sequana: a set of Snakemake NGS pipelines

Ultra-fast de novo assembler using long noisy reads

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

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

An accurate and ultra-fast hybrid genome assembler

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Long-reads Gap-free Chromosome-scale Assembler

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

Long Reads Annotation pipeline

Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome

Lima - Demultiplex Barcoded PacBio Samples

A Python library to visualize and analyze long-read transcriptomes

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

Close assembly gaps using long-reads at high accuracy.