Long read production pipelines
☆151Jul 27, 2026Updated this week
Alternatives and similar repositories for long-read-pipelines
Users that are interested in long-read-pipelines are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Comparison of multiple long read datasets☆177Jul 1, 2026Updated 3 weeks ago
- A catalogue of available long read sequencing data analysis tools☆90Updated this week
- Annotation and segmentation of MAS-seq data☆20May 25, 2023Updated 3 years ago
- Structural variant toolkit for VCFs☆420May 22, 2026Updated 2 months ago
- Variant calling tool for long-read sequencing data☆118Mar 19, 2025Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 8 months ago
- A tool for somatic structural variant calling using long reads☆174Jun 8, 2026Updated last month
- Plot structural variant signals from many BAMs and CRAMs☆572Jul 13, 2024Updated 2 years ago
- Simple pileup-based variant caller☆95Apr 25, 2025Updated last year
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆36Oct 27, 2025Updated 9 months ago
- deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads☆44Sep 5, 2022Updated 3 years ago
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆272Oct 13, 2022Updated 3 years ago
- Long read based human genomic structural variation detection with cuteSV☆291Jul 12, 2026Updated 2 weeks ago
- Hidden Markov Model based Copy number caller☆20Jul 18, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python☆30May 10, 2018Updated 8 years ago
- Structural variant (SV) analysis tools☆41Jul 1, 2024Updated 2 years ago
- pbsv - PacBio structural variant (SV) calling and analysis tools☆168Jul 15, 2026Updated 2 weeks ago
- Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)☆185Apr 12, 2023Updated 3 years ago
- Read-based phasing of genomic variants, also called haplotype assembly☆423Jul 4, 2026Updated 3 weeks ago
- Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling☆383Jul 9, 2026Updated 2 weeks ago
- ☆85Mar 3, 2025Updated last year
- Copy number caller for long read data including SNV utilization☆69Mar 31, 2025Updated last year
- Yet another k-mer analyzer☆173Dec 30, 2025Updated 6 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A fast approximate aligner for long DNA sequences☆289Oct 11, 2024Updated last year
- LongQC is a tool for the data quality control of the PacBio and ONT long reads.☆185Mar 25, 2026Updated 4 months ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆115Jun 6, 2021Updated 5 years ago
- a long read simulator that can imitate many types of read problems☆295Updated this week
- Plotting scripts for long read sequencing data☆557Jun 15, 2026Updated last month
- SV detection tool for nanopore sequence reads☆98Mar 25, 2026Updated 4 months ago
- Quality control tools for nanopore sequencing data☆114Oct 26, 2024Updated last year
- Nanopore sequence read simulator☆308Mar 12, 2026Updated 4 months ago
- Evaluation and polishing workflows for T2T genome assemblies☆160Jun 26, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Hybrid error correction of long reads using colored de Bruijn graphs☆108Jan 17, 2026Updated 6 months ago
- Annotation and Ranking of Structural Variation☆306Jun 19, 2026Updated last month
- WDL workflows for variant calling and assembly using ONT☆40Updated this week
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated 11 months ago
- SMRT-SV: Structural variant and indel caller for PacBio reads☆28Feb 21, 2019Updated 7 years ago
- Fast genome analysis from unassembled short reads☆324Apr 8, 2024Updated 2 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆241Dec 29, 2023Updated 2 years ago