Nanopore Python Packages

lib-pod5

Pod5: a high performance file format for nanopore reads.

escapepod

Rust library and CLI for pod5 manipulation, classification, and demux

pod5

Pod5: a high performance file format for nanopore reads.

pyspoa

Python bindings to spoa

sequali

Fast sequencing data quality metrics

dajin2

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

sniffles

Structural variation caller using third generation sequencing

medaka

Neural-network consensus polishing and variant calling for Oxford Nanopore sequencing data

deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

medaka-cpu

Neural-network consensus polishing and variant calling for Oxford Nanopore sequencing data

nanotimesort

Bin Oxford Nanopore reads by cumulative sequencing time intervals. Guppy, MinKNOW and Dorado compatible. Fast, streaming, zero dependencies.

pod5-format

Pod5: a high performance file format for nanopore reads.

deepchopper

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

poriscope

An extensible plugin-based analysis framework for nanopore data

pycoqc

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

ont-bonito

A PyTorch Basecaller for Oxford Nanopore Reads

ampligone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

isoquant

A universal toolkit for upstream processing of long RNA reads

dynamont

Dynamont is a bioinformatics tool for segmenting/resquiggling Oxford Nanopore Technologies (ONT) sequencing signals using dynamic programming and HMM-based approaches. It is designed to align raw nanopore signals to nucleotide sequences and supports DNA and RNA datasets.

ont-remora

Methylation/modified base calling separated from basecalling.

pynanolab

all in one GUI software for data analysis and visualization

deeprm

Deep learning for RNA Modification