JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
☆108Mar 20, 2026Updated this week
Alternatives and similar repositories for JAFFA
Users that are interested in JAFFA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing☆21Sep 19, 2021Updated 4 years ago
- ☆39Apr 25, 2023Updated 2 years ago
- EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2☆65Oct 11, 2024Updated last year
- fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector☆24Mar 9, 2026Updated 2 weeks ago
- De novo construction of isoforms from long-read data☆35Jun 10, 2025Updated 9 months ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- chimeraviz is an R package that automates the creation of chimeric RNA visualizations.☆39Nov 25, 2023Updated 2 years ago
- Full-length transcriptome splicing and mutation analysis☆87Jun 24, 2024Updated last year
- Detection of m6A from direct RNA-Seq data☆131May 19, 2025Updated 10 months ago
- Penguin: A Tool for Predicting Pseudouridine Sites in Direct RNA Nanopore Sequencing Data☆14Nov 15, 2021Updated 4 years ago
- A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.☆21Nov 20, 2022Updated 3 years ago
- RNA modification detection using Nanopore raw reads with Deep One Class classification☆20May 14, 2021Updated 4 years ago
- An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data☆15May 17, 2025Updated 10 months ago
- A tool to examine duplicate read characteristics in a BAM file☆12Dec 8, 2017Updated 8 years ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 7 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project☆153Jan 23, 2026Updated 2 months ago
- reference-free transcriptome assembly for short and long reads☆108Mar 13, 2026Updated last week
- diploid SNV caller for error-prone reads☆207Apr 26, 2024Updated last year
- Error correction of ONT transcript reads☆58Sep 6, 2023Updated 2 years ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆78Mar 21, 2023Updated 3 years ago
- Fast HLA type inference from whole-genome data☆143Apr 3, 2025Updated 11 months ago
- ☆24Dec 24, 2022Updated 3 years ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Oct 1, 2025Updated 5 months ago
- Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.☆105Jan 28, 2026Updated last month
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Long-read Isoform Quantification and Analysis☆38Mar 25, 2025Updated last year
- General purpose utility related to GAF files☆29Jan 27, 2026Updated last month
- De novo clustering of long transcript reads into genes☆70Apr 27, 2025Updated 10 months ago
- Split a BAM file by haplotype support☆16Dec 13, 2017Updated 8 years ago
- Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)☆205Mar 19, 2026Updated last week
- single-nucleus nanopore reads processing pipeline☆16Aug 16, 2023Updated 2 years ago
- Predicting oncogenic potential of gene fusions☆13Feb 13, 2016Updated 10 years ago
- Technology agnostic long read analysis pipeline for transcriptomes☆157Jan 25, 2024Updated 2 years ago
- modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data☆16Apr 29, 2024Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆268Mar 15, 2026Updated last week
- Full-Length Alternative Isoform analysis of RNA☆250Updated this week
- Gene Fusion Visualiser☆52Jan 15, 2023Updated 3 years ago
- SIMD partial order alignment tool/library☆176Sep 21, 2025Updated 6 months ago
- Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data☆71Mar 18, 2026Updated last week
- Structural Variant Identification Method using Long Reads☆181Jun 29, 2021Updated 4 years ago
- Identification of differential RNA modifications from nanopore direct RNA sequencing☆163Nov 7, 2024Updated last year