Assembly and binning of metagenomes

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

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

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

LongcallR is a SNP caller for single molecule long-read RNA-seq data

Long-read splice alignment with high accuracy

Single cell Nanopore sequencing data for Genotype and Phenotype

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

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

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

Fast and space-efficient taxonomic classification of long reads

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

Linear-time de novo Long Read Assembler

Clair3-RNA - a long-read small variant caller for RNA sequencing data

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

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