60 Open Source Nanopore Software Projects
Free and open source nanopore code projects including engines, APIs, generators, and tools.
Pycoqc 145 ⭐
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
Pipeline Structural Variation 94 ⭐
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Recentrifuge 65 ⭐
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Pipeline Transcriptome De 79 ⭐
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Epinano 65 ⭐
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
Comprna Rattle 31 ⭐
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
Pipeline Pinfish Analysis 26 ⭐
Pipeline for annotating genomes using long read transcriptomics data with pinfish
Fast Sg 20 ⭐
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
Awesome Sequencing Tech Papers 23 ⭐
A collection of publications on comparison of high-throughput sequencing technologies.
Taeper 17 ⭐
A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.
Tailfindr 24 ⭐
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
Fast5_fetcher 14 ⭐
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
Gtz 148 ⭐
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
Clair3 76 ⭐
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Parklab Xtea 39 ⭐
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Interartic 18 ⭐
InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
Marionilab Sarlacc 10 ⭐
The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, clusters reads and produces a consensus sequence for each cluster after multiple sequence alignment.