CMU-SAFARI / ScroogeLinks
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
☆38Updated 2 years ago
Alternatives and similar repositories for Scrooge
Users that are interested in Scrooge are comparing it to the libraries listed below
Sorting:
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆27Updated last year
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated 2 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆36Updated 4 months ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆23Updated this week
- URMAP ultra-fast read mapper☆38Updated 5 years ago
- QuickEd is a high-performance exact sequence alignment based on the bound-and-align paradigm.☆27Updated 4 months ago
- De Bruijn graph construction for large k.☆17Updated 4 years ago
- Benchmarking pairwise aligners☆36Updated 7 months ago
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Updated 3 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆50Updated 3 years ago
- Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.☆22Updated 7 years ago
- An experimental tool to estimate the similarity between all pairs of contigs☆34Updated 4 years ago
- A k-mer search engine for all Sequence Read Archive public accessions☆32Updated 10 months ago
- Profile HMM-based hybrid error correction algorithm for long reads☆21Updated 7 years ago
- Find Unique genomic Regions☆30Updated 2 weeks ago
- RabbitMash: an efficient highly optimized implementation of Mash.☆20Updated last year
- ☆28Updated 5 months ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆52Updated this week
- REINDEER REad Index for abuNDancE quERy☆56Updated 2 months ago
- GFA visualizer, GPU-accelerated using Vulkan☆72Updated 3 years ago
- A streaming method for mapping nanopore raw signals☆32Updated 3 years ago
- Efficient, parallel compression for terabyte-scale data☆48Updated 4 months ago
- Long read aligner for cyclic and acyclic pangenome graphs☆39Updated last year
- ☆14Updated 2 years ago
- Tumour-only somatic mutation calling using long reads☆27Updated 10 months ago
- C implementation of the Landau-Vishkin algorithm☆35Updated 3 years ago
- online notebooks for a review of genome sketching☆60Updated 5 years ago
- A fast seed-embed-extend based sequence mapper and aligner☆23Updated last year
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat☆23Updated 4 months ago