oxford-nanopore

There are 75 repositories under oxford-nanopore topic.

  • Nextomics/NextDenovo

    Fast and accurate de novo assembler for long reads

    Language:C3701420953

  • philres/ngmlr

    NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

    Language:C++2932210040

  • tjiangHIT/cuteSV

    Long read based human genomic structural variation detection with cuteSV

    Language:Python251612736

  • kishwarshafin/pepper

    PEPPER-Margin-DeepVariant

    Language:Python2441019742

  • bcgsc/NanoSim

    Nanopore sequence read simulator

    Language:Python2431817757
  • readfish

    LooseLab/readfish

    CLI tool for flexible and fast adaptive sampling on ONT sequencers

    Language:Python1691427534

  • mortazavilab/TALON

    Technology agnostic long read analysis pipeline for transcriptomes

    Language:Python137514531

  • nf-core/viralrecon

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

    Language:Nextflow125106164112

  • bcgsc/arcs

    🌈Scaffold genome sequence assemblies using linked or long read sequencing data

    Language:C++922410716

  • kishwarshafin/helen

    H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

    Language:Python696279

  • mortazavilab/TranscriptClean

    Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome

    Language:Python6763717
  • swan_vis

    mortazavilab/swan_vis

    A Python library to visualize and analyze long-read transcriptomes

    Language:Jupyter Notebook5742311

  • bcgsc/HLAminer

    ⛏ HLA predictions from NGS shotgun data

    Language:Perl5182615

  • refresh-bio/colord

    A versatile compressor of third generation sequencing reads.

    Language:C++494914

  • ksahlin/isONclust

    De novo clustering of long transcript reads into genes

    Language:Python485248

  • vpc-ccg/lordfast

    Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

    Language:C416154

  • andrewjpage/tiptoft

    Predict plasmids from uncorrected long read data

    Language:Python3941810

  • davidebolo1993/NanoR

    Nanopore data analysis in R

    Language:R3932310

  • BeatsonLab-MicrobialGenomics/micropipe

    A pipeline for high-quality bacterial genome construction using ONT sequencing

    Language:HTML38979

  • jonas-fuchs/varVAMP

    Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

    Language:Python33679
  • LRSDAY

    yjx1217/LRSDAY

    LRSDAY: Long-read Sequencing Data Analysis for Yeasts

    Language:Perl32289

  • yekaizhou/duet

    SNP-Assisted SV Calling and Phasing Using ONT

    Language:Python233132

  • aljpetri/isONform

    De novo construction of isoforms from long-read data

    Language:Python172102

  • unique379r/strspy

    STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio.

    Language:Shell16475

  • zhixingfeng/iGDA

    Detect and phase minor SNVs from long-read sequencing data

    Language:C++153100

  • AnjanaSenanayake/DeepSelectNet

    DeepSelecNet is an enhanced deep learning model to perform read classification for selective sequencing.

    Language:C14210

  • bsaintjo/slow5-rs

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

    Language:Rust10210

  • HMPNK/CSA2.6

    Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes

    Language:Perl10146

  • mbhall88/pistis

    Quality control plotting for long reads

    Language:Python10321

  • czmilanna/nanoforms

    The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

    Language:JavaScript9100

  • rnajena/read5

    Wrapper to read fast5, slow5, blow5 and pod5 files.

    Language:Python9121

  • YaoLi3/nanopore-methylation

    Long sequencing reads classifier

    Language:Python7304

  • rki-mf1/cievad

    A tool suite for a simple, streamlined and rapid evaluation of variant callsets

    Language:Nextflow63301

  • OpenOmics/modr

    An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

    Language:Python5121

  • rnajena/magnipore

    Magnipore: Differential single nucleotide changes of ONT signals

    Language:Red5210

  • simpsonlab/preqclr

    preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

    Language:C++4402