nf-core/mag

Assembly and binning of metagenomes

Language: Nextflow - Size: 19.3 MB - Last synced: about 6 hours ago - Pushed: about 7 hours ago - Stars: 183 - Forks: 97

HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Language: Python - Size: 3.2 MB - Last synced: about 21 hours ago - Pushed: 1 day ago - Stars: 220 - Forks: 26

nf-core/taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language: Nextflow - Size: 11.9 MB - Last synced: about 8 hours ago - Pushed: about 8 hours ago - Stars: 93 - Forks: 31

MicrobialDarkMatter/nanomotif

Nanomotif - a tool for identifying methylated motifs in metagenomic samples

Language: Python - Size: 8.64 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 13 - Forks: 0

CMU-SAFARI/RawHash

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/Supplement_1/i297/7210440)

Language: C - Size: 23 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 38 - Forks: 4

ablab/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language: Python - Size: 18.7 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 120 - Forks: 11

deepomicslab/SpecHLA

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

Language: C++ - Size: 156 MB - Last synced: about 9 hours ago - Pushed: 2 days ago - Stars: 22 - Forks: 8

wtsi-npg/valet

Automated data mangement for Oxford Nanopore DNA sequencing instruments

Language: Go - Size: 727 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 2 - Forks: 4

replikation/poreCov

SARS-CoV-2 workflow for nanopore sequence data

Language: Nextflow - Size: 28.4 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 39 - Forks: 15

mbhall88/pistis 📦

Quality control plotting for long reads

Language: Python - Size: 31.2 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 10 - Forks: 1

GoekeLab/awesome-nanopore

A curated list of awesome nanopore analysis tools.

Size: 112 KB - Last synced: 1 day ago - Pushed: 6 months ago - Stars: 213 - Forks: 38

justin-tpb/Vampyrellida-genomics

Scripts and data regarding Vampyrellida genomics.

Language: Shell - Size: 35.2 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

nanoporetech/dorado

Oxford Nanopore's Basecaller

Language: C++ - Size: 14.2 MB - Last synced: 3 days ago - Pushed: 7 days ago - Stars: 395 - Forks: 51

jazsakr/phd_vault

Size: 26.9 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 0

biocorecrg/MOP2

Master of Pores 2

Language: Nextflow - Size: 209 MB - Last synced: 3 days ago - Pushed: 6 months ago - Stars: 22 - Forks: 7

nf-core/viralrecon

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

Language: Nextflow - Size: 9.67 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 108 - Forks: 97

UPHL-BioNGS/Donut_Falls

Basic workflow for nanopore sequencing data

Language: Nextflow - Size: 1.25 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 12 - Forks: 1

nanoporetech/medaka

Sequence correction provided by ONT Research

Language: Python - Size: 62 MB - Last synced: 6 days ago - Pushed: 5 months ago - Stars: 384 - Forks: 72

nf-core/bacass

Simple bacterial assembly and annotation pipeline

Language: Nextflow - Size: 4.69 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 51 - Forks: 35

nanoporetech/pod5-file-format

Pod5: a high performance file format for nanopore reads.

Language: C++ - Size: 28.7 MB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 113 - Forks: 13

nanoporetech/bonito

A PyTorch Basecaller for Oxford Nanopore Reads

Language: Python - Size: 745 KB - Last synced: 3 days ago - Pushed: 5 months ago - Stars: 374 - Forks: 116

nanoporetech/pychopper 📦

A tool to identify, orient, trim and rescue full length cDNA reads

Language: Python - Size: 52 MB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 78 - Forks: 22

fritzsedlazeck/Sniffles

Structural variation caller using third generation sequencing

Language: Python - Size: 12.2 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 511 - Forks: 84

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

Language: Nextflow - Size: 20.8 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 3

WEHIGenomicsRnD/nanopore-transfer-automation

Performs archiving and transfer of Nanopore sequencing data

Language: Python - Size: 155 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 2 - Forks: 1

nanoporetech/rerio

Research release basecalling models and configurations

Language: Python - Size: 114 KB - Last synced: 7 days ago - Pushed: 5 months ago - Stars: 90 - Forks: 9

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

Language: Python - Size: 3.46 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 51 - Forks: 5

nanoporetech/modkit

A bioinformatics tool for working with modified bases

Language: Rust - Size: 196 MB - Last synced: 3 days ago - Pushed: 14 days ago - Stars: 105 - Forks: 4

xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

Language: Nextflow - Size: 2.47 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 2 - Forks: 1

Nazeeefa/awesome-sequencing-tech-papers

A collection of publications on comparison of high-throughput sequencing technologies.

Size: 163 KB - Last synced: 3 days ago - Pushed: 15 days ago - Stars: 26 - Forks: 3

marbl/Winnowmap

Long read / genome alignment software

Language: C - Size: 3.3 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 220 - Forks: 20

novoalab/modPhred

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

Language: Python - Size: 47.9 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 13 - Forks: 1

tleonardi/nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

Language: Python - Size: 138 MB - Last synced: 3 days ago - Pushed: 4 months ago - Stars: 75 - Forks: 12

novoalab/EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

Language: Python - Size: 5.12 GB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 102 - Forks: 32

mbhall88/taeper

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

Language: Python - Size: 1.34 MB - Last synced: 10 days ago - Pushed: about 6 years ago - Stars: 19 - Forks: 0

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Language: Python - Size: 1.93 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 29 - Forks: 2

remiolsen/anglerfish

Anglerfish - Nanopore reads from Illumina libraries

Language: Python - Size: 2.19 MB - Last synced: 23 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 3

parklab/xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

Language: Python - Size: 6.78 MB - Last synced: about 9 hours ago - Pushed: 3 months ago - Stars: 86 - Forks: 19

a-slide/pycoQC

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

Language: Python - Size: 180 MB - Last synced: 9 days ago - Pushed: 6 months ago - Stars: 238 - Forks: 38

akikuno/DAJIN2

🔬 Genotyping tool for genome-edited samples, utilizing nanopore sequencer target sequencing

Language: Python - Size: 556 MB - Last synced: about 22 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 0

nf-core/nanoseq

Nanopore demultiplexing, QC and alignment pipeline

Language: Nextflow - Size: 6.71 MB - Last synced: 3 days ago - Pushed: 7 days ago - Stars: 144 - Forks: 72

bsaintjo/cawlr-rs

Tool to analyze chromatin accessibility with long read sequencing technologies

Language: Jupyter Notebook - Size: 209 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 1

nanoporetech/remora

Methylation/modified base calling separated from basecalling.

Language: Python - Size: 44.5 MB - Last synced: 23 days ago - Pushed: 2 months ago - Stars: 139 - Forks: 17

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 327 KB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 7 - Forks: 0

adnaniazi/tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Language: R - Size: 18.6 MB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 49 - Forks: 15

nanoporetech/pipeline-structural-variation 📦

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Language: Python - Size: 6.22 MB - Last synced: 7 days ago - Pushed: over 2 years ago - Stars: 110 - Forks: 16

gaarangoa/argpore-cli

Client Serive of ARGpore pipeline for the analysis of antibiotic resistance in nanopore reads

Language: CSS - Size: 7.84 MB - Last synced: about 1 month ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

HKU-BAL/Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Language: Python - Size: 2.74 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

GoekeLab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Language: Jupyter Notebook - Size: 2.36 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 87 - Forks: 23

katerinakazantseva/stRainy

Graph-based assembly phasing

Language: Python - Size: 16.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 40 - Forks: 5

kishwarshafin/pepper

PEPPER-Margin-DeepVariant

Language: Python - Size: 36.1 MB - Last synced: 13 days ago - Pushed: 4 months ago - Stars: 231 - Forks: 41

comprna/RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Language: C++ - Size: 83 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 54 - Forks: 9

mbhall88/NanoVarBench

Evaluating Nanopore-based bacterial variant calling

Language: Python - Size: 34.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

mbhall88/ontime

Extract subsets of ONT (Nanopore) reads based on time

Language: Rust - Size: 146 KB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 16 - Forks: 1

ruanjue/wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Language: C - Size: 813 KB - Last synced: 25 days ago - Pushed: 8 months ago - Stars: 492 - Forks: 89

LRB-IIMCB/ninetails

An R package for finding non-adenosine residues in poly(A) tails of ONT direct RNA sequencing reads

Language: R - Size: 9.65 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 3

Psy-Fer/SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data

Language: Python - Size: 8.49 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 119 - Forks: 21

RIVM-bioinformatics/AmpliGone

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

Language: Python - Size: 2.54 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0

bsaintjo/slow5-rs

Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output

Language: Rust - Size: 986 KB - Last synced: 5 days ago - Pushed: 2 months ago - Stars: 9 - Forks: 0

nanoporetech/vbz_compression

VBZ compression plugin for nanopore signal data

Language: C++ - Size: 3.81 MB - Last synced: 1 day ago - Pushed: almost 2 years ago - Stars: 38 - Forks: 9

nf-core/detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

Language: Nextflow - Size: 4.16 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 9 - Forks: 3

khyox/recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Language: Python - Size: 13.3 MB - Last synced: 10 days ago - Pushed: 3 months ago - Stars: 84 - Forks: 6

comprna/CHEUI

Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing

Language: C++ - Size: 50 MB - Last synced: 27 days ago - Pushed: 12 months ago - Stars: 24 - Forks: 2

Yedomon/Benchmarking-long-reads-assemblers-for-Fusarium-oxysporum-genus-genome-assembly

Benchmarking for long-reads assembler

Size: 168 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 5 - Forks: 0

GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

Language: Python - Size: 4.96 MB - Last synced: 3 days ago - Pushed: 18 days ago - Stars: 127 - Forks: 22

karel-brinda/NanoSim-H

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

Language: Python - Size: 1.46 MB - Last synced: 18 days ago - Pushed: over 1 year ago - Stars: 16 - Forks: 6

guangzhaocs/bioinformatics-starter

Quickstart to Bioinformatics & Biomedical AI.

Language: Python - Size: 278 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

usnistgov/mosaic

A modular single-molecule analysis interface

Language: Python - Size: 308 MB - Last synced: 4 days ago - Pushed: 10 months ago - Stars: 37 - Forks: 17

hasindu2008/squigulator

a tool for simulating nanopore raw signal data

Language: C - Size: 17.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 56 - Forks: 2

chanzuckerberg/shasta 📦

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Language: C++ - Size: 11.2 MB - Last synced: 24 days ago - Pushed: over 1 year ago - Stars: 269 - Forks: 56

hyeshik/poreplex

A versatile sequenced read processor for nanopore direct RNA sequencing

Language: Python - Size: 14.5 MB - Last synced: 7 days ago - Pushed: almost 4 years ago - Stars: 77 - Forks: 13

fmalmeida/MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

Language: Nextflow - Size: 83.4 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 49 - Forks: 10

comprna/riser

Biochemical-free targeting of RNA classes during direct RNA sequencing

Language: Python - Size: 203 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 9 - Forks: 2

FOI-Bioinformatics/nanometa_live

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.

Language: Python - Size: 1.45 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 9 - Forks: 2

esteinig/sketchy

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

Language: Rust - Size: 20 MB - Last synced: 11 days ago - Pushed: over 1 year ago - Stars: 43 - Forks: 3

Runsheng/trackcluster

An analysis pipeline for Nanopore direct-RNA sequencing

Language: Python - Size: 3.4 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 10 - Forks: 3

nanoporetech/pipeline-transcriptome-de 📦

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Language: Python - Size: 124 KB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 105 - Forks: 25

MorrellLAB/sequence_handling Fork of pmorrell/sequence_handling

A series of scripts to automate sequence workflows

Language: Jupyter Notebook - Size: 6.94 MB - Last synced: 2 months ago - Pushed: 4 months ago - Stars: 18 - Forks: 9

nanoporetech/wub 📦

Tools and software library developed by the ONT Applications group

Language: Python - Size: 385 KB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 61 - Forks: 10

galantelab/sandy

A straightforward and complete next-generation sequencing read simulator

Language: Perl - Size: 25.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 15 - Forks: 2

lucast122/MMonitor

Software for monitoring metagenomes using nanopore sequencing reads

Language: C - Size: 156 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

quadram-institute-bioscience/dorado-gpu-testing Fork of thanhleviet/dorado-gpu-testing

Benchmarking several NVIDIA GPUs with dorado

Language: Python - Size: 445 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

thanhleviet/dorado-gpu-testing

Benchmarking several NVIDIA GPUs with dorado

Language: Python - Size: 445 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

MHH-RCUG/Wochenende

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Language: Python - Size: 40.7 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 37 - Forks: 16

projectoriented/methylink

CLI tool to link methylation tags between two files

Language: Python - Size: 183 MB - Last synced: 19 days ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

marcpaga/sturgeon

Sturgeon is a CNS neural network classifier

Language: Python - Size: 91 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 19 - Forks: 5

nf-core/denovohybrid Fork of caspargross/nf-core-denovohybrid 📦

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

Language: Nextflow - Size: 2.55 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3

Genetalks/gtz

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

Size: 1.53 GB - Last synced: 8 days ago - Pushed: about 2 years ago - Stars: 170 - Forks: 39

igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

Language: R - Size: 241 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 182 - Forks: 51

ahcm/longread_plots

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

Language: Python - Size: 593 KB - Last synced: 10 days ago - Pushed: over 1 year ago - Stars: 12 - Forks: 0

novoalab/m6ABasecaller

An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

Size: 19.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 7 - Forks: 0

3w1714n0/Benchmark_Analysis_full-length_isoforms

Benchmark analysis of algorithms for determining full-length mRNA isoforms by Nanopore RNA-seq data.

Language: R - Size: 262 KB - Last synced: 4 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

Han-Cao/HarmoniSV

A toolkit to harmonize and filter structural variations across methods and samples.

Language: Python - Size: 5.51 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

quadram-institute-bioscience/galaxy-tools

A collection of bioinformatics tools for use with galaxy written at Quadram Institute

Language: HTML - Size: 295 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 4 - Forks: 3

Psy-Fer/interARTIC

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Language: CSS - Size: 85.3 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 24 - Forks: 3

nanoporetech/pipeline-pinfish-analysis 📦

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Language: Python - Size: 137 KB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 27 - Forks: 5

lfaino/LoReAn

Long Reads Annotation pipeline

Language: Python - Size: 467 MB - Last synced: 3 months ago - Pushed: about 2 years ago - Stars: 68 - Forks: 10

HKU-BAL/ClusterV

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

Language: Python - Size: 13.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 5 - Forks: 0

yanhui09/laca

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)

Language: Python - Size: 124 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 5 - Forks: 2

garcia-nacho/Wastewater_SARS-CoV-2

Surveillance of wastewater for SARS-CoV-2 detection

Language: R - Size: 18.2 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 1