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Kirilllive /tuesday-js

Star622

simple web-based, free and open-source visual novel editor that can be used in a web browser. It is written in JavaScript without using any third party libraries and thus does not require additional software installation. The engine uses standard HTML document elements such as div and img.

storytelling interactive-fiction literate-programming long-read visual-novel adventure-game-engine interactive-storytelling web-editor visual-novels single-page-applications web-based-game visual-novel-engine screenplay creative-writing nocode web-based-application visual-novel-maker edutainment visual-novel-editor

UpdatedFeb 19, 2026
HTML

philres /ngmlr

Star307

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

docker mapper next-generation-sequencing alignment long-read pacbio bioconda oxford-nanopore structural-variations

UpdatedMar 18, 2024
C++

chanzuckerberg /shasta

Star274

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

nanopore assembly sequencing dna long-read pacbio de-novo

UpdatedOct 13, 2022
C++

marbl /SALSA

Star188

SALSA: A tool to scaffold long read assemblies with Hi-C data

assembly scaffold long-read hic

UpdatedMay 17, 2024
Python

kcleal /dysgu

Star115

Toolkit for calling structural variants using short or long reads

bioinformatics genomics long-read variant-calling variant structural-variation paired-end structural

UpdatedFeb 11, 2026
Cython

mortazavilab /swan_vis

Star66

A Python library to visualize and analyze long-read transcriptomes

bioinformatics long-read pacbio transcriptome oxford-nanopore pacbio-iso-seq

UpdatedJan 19, 2026
Jupyter Notebook

PASSIONLab /BELLA

Star52

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

matrix-multiplication long-read read-aligners spgemm genome-alignment overlapper pacbio-aligner longread-aligner

UpdatedMay 16, 2022
C++

JensUweUlrich /Taxor

Star43

Fast and space-efficient taxonomic classification of long reads

bioinformatics taxonomy metagenomics long-read microbiome kmer em-algorithm taxonomic-classification refseq bioinf long-read-sequencing xor-filter taxonomic-profiling syncmer pseudo-alignment interleaved-xor-filter

UpdatedAug 25, 2025
C++

vpc-ccg /lordfast

Star40

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

mapping long-read pacbio oxford-nanopore single-molecule-sequencing

UpdatedJul 15, 2019
C

Clinical-Genomics /stranger

Star39

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

bioinformatics long-read long-read-sequencing short-tandem-repeats massively-parallel-sequencing

UpdatedDec 15, 2025
Python

jteutenberg /downpore

Star31

Suite of tools for use in genome assembly and consensus. Work in progress.

long-read genome-assembly genome-scaffolding genome-mapping

UpdatedMar 22, 2021
Go

fairliereese /LR-splitpipe

Star24

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

rna-seq long-read transcriptome single-cell demultiplexing

UpdatedOct 19, 2023
Python

nf-core /methylong

Star20

Extract methylation calls from long reads (ONT/ PacBio)

workflow pipeline nextflow long-read pacbio dna-methylation ont nf-core fiber-seq

UpdatedDec 19, 2025
Nextflow

guigolab /tmerge

Star20

Merge transcriptome read-to-genome alignments into non-redundant transcript models

bioinformatics genomics genome sequencing merge long-read transcriptome transcriptomics

UpdatedJan 21, 2026

comprna /R2Dtool

Star18

Analyse RNA feature distributions.

rna-seq nanopore long-read transcriptomics epitranscriptomics

UpdatedDec 16, 2024
Jupyter Notebook

PacificBiosciences /minorseq

Star15

Minor Variant Calling and Phasing Tools

statistics next-generation-sequencing haplotypes long-read pacbio minor-variant phasing drug-resistance

UpdatedJan 13, 2022

nf-core /pacvar

Star13

Longread PacBio sequencing processing for WGS and PureTarget

workflow pipeline nextflow alignment long-read pacbio variant-calling wgs nf-core puretarget

UpdatedJan 13, 2026
Nextflow

zouyinstein /hifisr

Star10

HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).

variants long-read arabidopsis heteroplasmy mitochondrial-genomes