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Nextomics /NextDenovo

Star389

Fast and accurate de novo assembler for long reads

assembler pacbio oxford-nanopore genome-assembly long-reads

UpdatedMay 10, 2024
C

HKU-BAL /Clair3

Star276

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

deep-learning nanopore genomics computational-biology pacbio variant-calling illumina long-reads variant-detection ont-data ont-models

UpdatedApr 14, 2025
Python

kishwarshafin /pepper

Star248

PEPPER-Margin-DeepVariant

nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing

UpdatedJan 12, 2024
Python

GoekeLab /bambu

Star206

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

rna-seq r nanopore bioconductor transcriptomics rna-seq-analysis transcript-quantification bambu long-reads nanopore-sequencing transcript-reconstruction

UpdatedApr 16, 2025
R

broadinstitute /long-read-pipelines

Star145

Long read production pipelines

pipelines wdl variant-calling de-novo-assembly long-reads

UpdatedApr 24, 2025
Jupyter Notebook

nf-core /taxprofiler

Star144

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

workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling microbiome illumina long-reads taxonomic-classification nf-core taxonomic-profiling

UpdatedApr 24, 2025
Nextflow

GoekeLab /sg-nex-data

Star127

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

rna-seq nanopore transcriptomics long-reads direct-rna-sequencing

UpdatedJan 15, 2025
R

yangao07 /abPOA

Star120

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

simd long-reads multiple-sequence-alignment partial-order-alignment consensus-sequences banded-dp consensus-sequence alignment-graph gfa-format

UpdatedMar 23, 2025
C

nanoporetech /pipeline-structural-variation

Star114

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

nanopore whole-genome-sequencing structural-variation long-reads

UpdatedOct 25, 2021
Python

bcgsc /straglr

Star103

Tandem repeat expansion detection or genotyping from long-read alignments

bioinformatics genomics tandem-repeats long-reads

UpdatedFeb 7, 2025
Python

HKU-BAL /ClairS

Star83

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

bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads

UpdatedApr 23, 2025
Python

katerinakazantseva /strainy

Star80

Graph-based assembly phasing

nanopore assembly sequencing metagenomics metagenomic-analysis long-reads hifi long-read-sequencing

UpdatedApr 25, 2025
Python

MeHelmy /princess

Star79

methylation phasing structural-variation long-reads single-nucleotide-variation

UpdatedMar 3, 2025
Python

ganlab /GALA

Star79

Long-reads Gap-free Chromosome-scale Assembler

nanopore pacbio scaffolding genome-analysis genome-assembly long-reads gap-filling

UpdatedMar 21, 2023
Python

natir /yacrd

Star78

Yet Another Chimeric Read Detector

bioinformatics chimera sequence long-reads

UpdatedNov 7, 2024
Rust

vpc-ccg /haslr

Star77

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

bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

UpdatedApr 22, 2020
C++

bcgsc /LINKS

Star74

⛓ Long Interval Nucleotide K-mer Scaffolder

bloom-filter scaffold long-reads draft-assembly extract-kmer-pairs genome-assemblies scaffold-layout

UpdatedApr 1, 2025
Perl

HKU-BAL /ClairS-TO

Star60

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

bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina snvs long-reads ont long-read-sequencing tumors tumor-only

UpdatedMar 25, 2025
Python

muellan /metacache

Star59

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

bioinformatics genome taxonomy metagenomics classification fasta fastq metagenomes dna-sequences short-read-mapper read-mapping metagenomic-analysis metagenomic-classification genomic-data-analysis bioinformatics-algorithms long-reads metagenomic-data refseq ncbi-refseq bioinformatics-tool

UpdatedApr 2, 2025
C++

morispi /CONSENT

Star55

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

assembly ngs consensus correction long self msa reads contigs long-reads multiple-sequence-alignment polishing self-correction

UpdatedFeb 6, 2024
C++

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