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af-ns

cellcontrast

CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning

chromatin-fiber-imaging

Chromatin Fiber Imaging

chromseg

A framework for crossing-overlap chromosome segmentation

clair

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

clair3

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

clair3-mp

variant calling using with sequencing data from multiple platforms

clair3-nova

de novo variant calling in trio using Nanopore long-reads

clair3-rna

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

clair3-trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

clairs

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

clairs-to

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

clairvoyante-pytroch

Pytorch version of Clairvoyante

clusterv

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

clusterv-web

connet

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

cpg

Building a Chinese pan-genome of 486 individuals

ecnano

A target captured medical exome ONT sequencing with amplicon variant calling workflow

hkg

megabox

A web platform for hosting up-to-date MEGAHIT assemblies of publicly available but challenging metagenome sequence data.

megagta

HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs

megapath

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

megapath-nano

MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics; MegaPath-Nano-Amplicon: filtering module for metagenomic amplicon data

ncov19_cytosine_depletion

ont-tb-nf

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

sensv

A tool to detect structural variant

tc-reno

A tool to detect full length isoforms of RNA

translocator

Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads

uncalled

Raw nanopore signal mapper that enables real-time targeted sequencing