nanopore
There are 226 repositories under nanopore topic.
fritzsedlazeck/Sniffles
Structural variation caller using third generation sequencing
ruanjue/wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
nanoporetech/dorado
Oxford Nanopore's Basecaller
nanoporetech/medaka
Sequence correction provided by ONT Research
nanoporetech/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
chanzuckerberg/shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
a-slide/pycoQC
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
kishwarshafin/pepper
PEPPER-Margin-DeepVariant
marbl/Winnowmap
Long read / genome alignment software
HKU-BAL/Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
GoekeLab/awesome-nanopore
A curated list of awesome nanopore analysis tools.
igordot/genomics
A collection of scripts and notes related to genomics and bioinformatics
nf-core/mag
Assembly and binning of metagenomes
Genetalks/gtz
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
GoekeLab/bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
nanoporetech/remora
Methylation/modified base calling separated from basecalling.
GoekeLab/xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
ablab/IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Psy-Fer/SquiggleKit
SquiggleKit: A toolkit for manipulating nanopore signal data
nanoporetech/pod5-file-format
Pod5: a high performance file format for nanopore reads.
nanoporetech/modkit
A bioinformatics tool for working with modified bases
nanoporetech/pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
novoalab/EpiNano
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
nanoporetech/pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nanoporetech/rerio
Research release basecalling models and configurations
GoekeLab/sg-nex-data
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
giesselmann/nanopype
Snakemake pipelines for nanopore sequencing data archiving and processing
parklab/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
khyox/recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
adigenova/wengan
An accurate and ultra-fast hybrid genome assembler
hyeshik/poreplex
A versatile sequenced read processor for nanopore direct RNA sequencing
nanoporetech/pychopper
A tool to identify, orient, trim and rescue full length cDNA reads
tleonardi/nanocompore
RNA modifications detection from Nanopore dRNA-Seq data