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

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

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.

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

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

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

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

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Coronavirus (SARS-Cov-2) sequencing analysis

Transcriptome long-read orientation with Deep Learning

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

🔬 Genotyping tool for genome-edited samples, utilizing nanopore sequencer target sequencing

Lightweight bioinformatics pipeline for microbial genome recovery