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Search results for nanopore
nanopore
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109 search results found
Sniffles
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479
Structural variation caller using third generation sequencing
Wtdbg2
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401
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
Medaka
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359
Sequence correction provided by ONT Research
Bonito
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354
A PyTorch Basecaller for Oxford Nanopore Reads
Dorado
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309
Oxford Nanopore's Basecaller
Shasta
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269
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Pepper
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216
PEPPER-Margin-DeepVariant
Pycoqc
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213
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
Clair3
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191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Awesome Nanopore
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175
A curated list of awesome nanopore analysis tools.
Mag
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164
Assembly and binning of metagenomes
Gtz
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156
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
Genomics
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154
A collection of scripts and notes related to genomics and bioinformatics
Bambu
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150
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Winnowmap
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131
Long read / genome alignment software
Nanoseq
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122
Nanopore demultiplexing, QC and alignment pipeline
Xpore
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122
Identification of differential RNA modifications from nanopore direct RNA sequencing
Remora
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120
Methylation/modified base calling separated from basecalling.
Squigglekit
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106
SquiggleKit: A toolkit for manipulating nanopore signal data
Viralrecon
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101
Assembly and intrahost/low-frequency variant calling for viral samples
Isoquant
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98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Pod5 File Format
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97
Pod5: a high performance file format for nanopore reads.
Pipeline Transcriptome De
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95
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Epinano
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94
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
Pipeline Structural Variation
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87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Recentrifuge
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83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Sg Nex Data
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80
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
Rerio
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80
Research release basecalling models and configurations
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Nanopype
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78
Snakemake pipelines for nanopore sequencing data archiving and processing
Pychopper
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74
A tool to identify, orient, trim and rescue full length cDNA reads
Xtea
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70
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Modkit
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68
A bioinformatics tool for working with modified bases
Lorean
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62
Long Reads Annotation pipeline
Wengan
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57
An accurate and ultra-fast hybrid genome assembler
Nanocompore
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56
RNA modifications detection from Nanopore dRNA-Seq data
Wub
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52
Tools and software library developed by the ONT Applications group
Poreplex
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51
A versatile sequenced read processor for nanopore direct RNA sequencing
Rattle
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51
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
Mpgap
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51
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
Bacass
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47
Simple bacterial assembly and annotation pipeline
Gala
⭐
45
Long-reads Gap-free Chromosome-scale Assembler
Clairs
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42
ClairS - a deep-learning method for long-read somatic small variant calling
Squigulator
⭐
40
a tool for simulating nanopore raw signal data
Haslr
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39
A fast tool for hybrid genome assembly of long and short reads
Porecov
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38
SARS-CoV-2 workflow for nanopore sequence data
Pinfish
⭐
36
Tools to annotate genomes using long read transcriptomics data
Mosaic
⭐
36
A modular single-molecule analysis interface
Strique
⭐
35
Nanopore raw signal repeat detection pipeline
Sketchy
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35
Genomic neighbor typing of bacterial pathogens using MinHash 🐀
Strainy
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33
Graph-based assembly phasing
Tailfindr
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32
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
Rkmh
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32
Classify sequencing reads using MinHash.
Wochenende
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30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
Interartic
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29
InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
Vbz_compression
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26
VBZ compression plugin for nanopore signal data
Mmlong2
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26
An all-in-one genome-centric metagenomics workflow using long reads
Awesome Sequencing Tech Papers
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26
A collection of publications on comparison of high-throughput sequencing technologies.
Pyguppyclient
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25
Python client library for Guppy
Rawhash
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23
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39
Pipeline Pinfish Analysis
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22
Pipeline for annotating genomes using long read transcriptomics data with pinfish
Mop2
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20
Master of Pores 2
Nanoflow
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20
🔬 De novo assembly of nanopore reads using nextflow
Tiptoft
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20
Predict plasmids from uncorrected long read data
Porefile
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19
A Nextflow full-length 16S profiling pipeline for ONT reads
Sturgeon
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18
Clairs To
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18
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
Taeper
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16
A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.
Fast Sg
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16
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
Spechla
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15
SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events.
Sandy
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14
A straightforward and complete next-generation sequencing read simulator
Dena
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14
Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
Container_recipes
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14
Repository with all my container recipes 👩🍳
Streamformatics
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13
Real-time species-typing visualisation for nanopore data.
Modphred
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12
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
Clair3 Trio
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12
Clair3-Trio: variant calling in trio using Nanopore long-reads
Sequence_handling
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12
A series of scripts to automate sequence workflows
Pyspoa
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12
Python bindings to spoa
Ontime
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11
Extract subsets of ONT (Nanopore) reads based on time
Fast5seek
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11
Subset of fast5 files contained in a fastq, BAM, or SAM file.
Cheui
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11
Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing
Guppy_on_slurm
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10
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
Npore
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10
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
Dinopore
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10
DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing
Pynanolab
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10
all in one GUI software for data analysis and visualization
Longread_plots
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10
A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.
Trackcluster
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9
An analysis pipeline for Nanopore direct-RNA sequencing
Fast5_fetcher
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9
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
Monica
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9
MinION Open Nucleotide Identifier for Continuous Analysis - an open source pathogen identifier for real-time analysis on MinION output
Tbpore
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9
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
Nanosim H
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8
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
Nanometa_live
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7
A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.
M6abasecaller
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7
An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)
Nanoplexer
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6
Tool for demultiplexing Nanopore barcode sequence data
Ampligone
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6
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
Ont Analysis Toolkit
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6
A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.
Nanotail
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6
R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions
Donut_falls
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6
Basic workflow for nanopore sequencing data
Clair3 Rna
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5
Clair3-RNA - long-read short variant caller for RNA sequencing data
Pistis
⭐
5
Quality control plotting for long reads
1-100 of 109 search results
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