DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Assembly and binning of metagenomes

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

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

Graph-based assembly phasing

Long-read splice alignment with high accuracy

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

Fast and space-efficient taxonomic classification of long reads

Single cell Nanopore sequencing data for Genotype and Phenotype

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

A pipeline for high-quality bacterial genome construction using ONT sequencing

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

Linear-time de novo Long Read Assembler

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

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

NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)

An algorithm for centromere assembly using long error-prone reads

A collection of publications on comparison of high-throughput sequencing technologies.