oxford-nanopore

Fast and accurate de novo assembler for long reads

Nanopore sequence read simulator

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

Long read based human genomic structural variation detection with cuteSV

PEPPER-Margin-DeepVariant

CLI tool for flexible and fast adaptive sampling on ONT sequencers

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

Technology agnostic long read analysis pipeline for transcriptomes

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

De novo clustering of long transcript reads into genes

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome

A Python library to visualize and analyze long-read transcriptomes

⛏ HLA predictions from NGS shotgun data

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

A versatile compressor of third generation sequencing reads.

De novo construction of isoforms from long-read data

Nanopore data analysis in R

Predict plasmids from uncorrected long read data

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