Structural variation caller using third generation sequencing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Fast and accurate de novo assembler for long reads

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

Long read / genome alignment software

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

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

Amplicon sequencing analysis workflow using DADA2 and QIIME2

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

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

Sequana: a set of Snakemake NGS pipelines

Technology agnostic long read analysis pipeline for transcriptomes

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

An accurate and ultra-fast hybrid genome assembler

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

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