cucapra / pollenLinks
generating hardware accelerators for pangenomic graph queries
☆38Updated last week
Alternatives and similar repositories for pollen
Users that are interested in pollen are comparing it to the libraries listed below
Sorting:
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆52Updated 2 years ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆29Updated 2 years ago
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆34Updated 9 months ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Updated 2 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 6 years ago
- GFA visualizer, GPU-accelerated using Vulkan☆73Updated 3 years ago
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆17Updated 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
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆51Updated 3 years ago
- RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genome…☆57Updated last month
- Rust implementation of VG handle graph☆20Updated last year
- ☆14Updated 8 months ago
- GFA parser in Rust☆31Updated 2 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆20Updated 2 months ago
- De Bruijn graph construction for large k.☆18Updated 3 years ago
- ☆16Updated 4 years ago
- Hardware Accelerated Read Until☆15Updated 2 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated last year
- ☆17Updated 2 years ago
- Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a sing…☆27Updated 5 years ago
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 3 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆36Updated 3 months ago
- 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
- QuickEd is a high-performance exact sequence alignment based on the bound-and-align paradigm.☆27Updated 3 months ago
- ☆17Updated 2 years ago
- Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., "SeGraM: A Universal Hardware …☆12Updated 2 years ago
- A toolkit for exploring regions of variation in a variation graph☆11Updated this week
- genome variation graphs constructed from HLA GRCh38 ALTs☆23Updated 3 years ago
- Benchmarking pairwise aligners☆36Updated 6 months ago
- Complements Minimap2 for a fast and efficient Read-Until pipeline☆12Updated 2 years ago