Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improvements on top of GenASM, and high-performance CPU and GPU implementations. Described by Lindegger et al. at https://doi.org/10.48550/arXiv.2208.09985
☆38Jun 23, 2023Updated 3 years ago
Alternatives and similar repositories for Scrooge
Users that are interested in Scrooge are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆47May 10, 2023Updated 3 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 9 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆27Apr 29, 2024Updated 2 years ago
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆28May 23, 2024Updated 2 years ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated 3 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- For bluntifying overlapped GFAs☆13Jul 26, 2024Updated 2 years ago
- De novo genome assembler.☆12Jul 30, 2018Updated 7 years ago
- Error correction of long reads☆16Jan 30, 2026Updated 5 months ago
- ☆11Dec 9, 2022Updated 3 years ago
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- ☆68Apr 9, 2024Updated 2 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆95Updated this week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- The Modular Aligner and The Modular SV Caller☆47Jul 18, 2023Updated 3 years ago
- Tools to gather evidence for structural variation via breakpoint detection.☆21Mar 27, 2026Updated 4 months ago
- Correction of palindromes in long reads from PacBio and Nanopore☆14Mar 1, 2022Updated 4 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆56May 17, 2022Updated 4 years ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆57Mar 7, 2025Updated last year
- Lift-over alignments from variant-aware references☆34Mar 4, 2023Updated 3 years ago
- Extracts subgraphs or components from a graph in GFA format☆24Nov 18, 2024Updated last year
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- SRF: Satellite Repeat Finder☆107Jan 8, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 8 months ago
- Iterative error correction of long reads☆13Dec 9, 2022Updated 3 years ago
- PyGim is the first runtime framework to efficiently execute Graph Neural Networks (GNNs) on real Processing-in-Memory systems. It provide…☆36Apr 23, 2025Updated last year
- de Bruijn Graph-based read aligner☆36Sep 3, 2018Updated 7 years ago
- Hidden Markov Model based Copy number caller☆20Jul 18, 2026Updated last week
- vcfdist: Accurately benchmarking phased variant calls☆87Jul 18, 2026Updated last week
- A pairwise sequence aligner written in Rust☆153May 22, 2026Updated 2 months ago
- Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal pa…☆36Mar 29, 2020Updated 6 years ago
- A Rust implementation of SSHash☆19Jul 2, 2026Updated 3 weeks ago
- 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.
- Linear-time de novo Long Read Assembler☆42Mar 19, 2026Updated 4 months ago
- Scaffolding with assembly likelihood optimization☆21Dec 14, 2020Updated 5 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- drunk on perbase pileups and lua expressions☆19Nov 15, 2025Updated 8 months ago
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆23Apr 12, 2023Updated 3 years ago
- Toolkit for calling structural variants using short or long reads☆115Jul 14, 2026Updated 2 weeks ago
- Graph based multi genome aligner☆49Sep 17, 2021Updated 4 years ago