long-reads

There are 83 repositories under long-reads topic.

  • Nextomics/NextDenovo

    Fast and accurate de novo assembler for long reads

    Language:C3471420252

  • kishwarshafin/pepper

    PEPPER-Margin-DeepVariant

    Language:Python2301019541

  • HKU-BAL/Clair3

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

    Language:Python2251026627
  • bambu

    GoekeLab/bambu

    Reference-guided transcript discovery and quantification for long read RNA-Seq data

    Language:R167717821

  • broadinstitute/long-read-pipelines

    Long read production pipelines

    Language:Jupyter Notebook1261616123

  • nanoporetech/pipeline-structural-variation

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

    Language:Python111292216

  • yangao07/abPOA

    abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

    Language:C10985818

  • nf-core/taxprofiler

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

    Language:Nextflow10314718733
  • sg-nex-data

    GoekeLab/sg-nex-data

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

    Language:Jupyter Notebook9471823

  • MeHelmy/princess

    Language:Python795169

  • vpc-ccg/haslr

    A fast tool for hybrid genome assembly of long and short reads

    Language:C++746379

  • natir/yacrd

    Yet Another Chimeric Read Detector

    Language:Rust723468

  • bcgsc/LINKS

    ⛓ Long Interval Nucleotide K-mer Scaffolder

    Language:Perl70115915

  • ganlab/GALA

    Long-reads Gap-free Chromosome-scale Assembler

    Language:Python6743315

  • HKU-BAL/ClairS

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

    Language:Python565255

  • muellan/metacache

    memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

    Language:C++5674012

  • morispi/CONSENT

    Scalable long read self-correction and assembly polishing with multiple sequence alignment

    Language:C++544354

  • bcgsc/straglr

    Tandem repeat expansion detection or genotyping from long-read alignments

    Language:Python496349
  • dentist

    a-ludi/dentist

    Close assembly gaps using long-reads at high accuracy.

    Language:D474426

  • CMU-SAFARI/SneakySnake

    SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.

    Language:VHDL469311

  • refresh-bio/colord

    A versatile compressor of third generation sequencing reads.

    Language:C++464911

  • katerinakazantseva/strainy

    Graph-based assembly phasing

    Language:Python415274

  • andrewjpage/tiptoft

    Predict plasmids from uncorrected long read data

    Language:Python3841810

  • HKU-BAL/ClairS-TO

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

    Language:Python362103

  • smehringer/SViper

    Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

    Language:C++325108

  • orangeSi/GSSplayground

    Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

    Language:HTML31507

  • bcgsc/ntLink

    Minimizer-based assembly scaffolding and mapping using long reads

    Language:Python289117

  • fritzsedlazeck/SVCollector

    Method to optimally select samples for validation and resequencing

    Language:C++26425

  • quadram-institute-bioscience/socru

    Order and orientation of complete bacterial genomes

    Language:Python264116

  • seryrzu/centroFlye

    An algorithm for centromere assembly using long error-prone reads

    Language:Python265175

  • algbio/GraphChainer

    An accurate aligner of long reads to a variation graph, based on co-linear chaining

    Language:C++25464

  • lpryszcz/pyScaf

    Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.

    Language:Python2561111

  • yangao07/TideHunter

    TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

    Language:C245114

  • at-cg/minichain

    Long-read aligner to pangenome graphs

    Language:C23422

  • mortazavilab/lapa

    Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

    Language:Jupyter Notebook2211512

  • natir/rustyread

    A long read simulator based on badread idea

    Language:Jupyter Notebook21232