Alternatives and similar repositories for gpuPairHMM:

Users that are interested in gpuPairHMM are comparing it to the libraries listed below

• asbschmidt / CUDASW4
  CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search
  ☆36Updated 4 months ago
• albertozeni / LOGAN
  LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.
  ☆29Updated 2 years ago
• IntelLabs / GKL
  Accelerated kernel library for genomics
  ☆106Updated last week
• quim0 / WFA-GPU
  GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
  ☆33Updated 6 months ago
• nahmedraja / GASAL2
  ☆46Updated 2 years ago
• ljdursi / poapy
  A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes
  ☆73Updated 9 months ago
• EIHealth-Lab / fast-bonito
  ☆25Updated 4 years ago
• PASSIONLab / BELLA
  BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
  ☆48Updated 2 years ago
• minhhpham / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆17Updated last year
• CMU-SAFARI / SeGraM
  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
• ratschlab / metagraph
  Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
  ☆118Updated last week
• lh3 / ksw2
  Global alignment and alignment extension
  ☆131Updated last year
• IntelLabs / Open-Omics-Acceleration-Framework
  Intel lab's open sourced data science framework for accelerating digital biology
  ☆44Updated last month
• MauricioCarneiro / PairHMM
  Optimization of a Haplotype PairHMM class for GPU processing
  ☆24Updated 8 years ago
• UCLA-VAST / minimap2-acceleration
  Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository
  ☆33Updated 4 months ago
• IntelLabs / Trans-Omics-Acceleration-Library
  ☆16Updated 10 months ago
• CMU-SAFARI / Scrooge
  Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…
  ☆37Updated last year
• lvrcek / GNNome-assembly
  Learning to untangle genome assembly with graph neural networks.
  ☆72Updated 4 months ago
• COMBINE-lab / pufferfish
  An efficient index for the colored, compacted, de Bruijn graph
  ☆108Updated 5 months ago
• COMBINE-lab / cuttlefish
  Building the compacted de Bruijn graph efficiently from references or reads.
  ☆86Updated last month
• NVlabs / nvbio-gpl
  NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.
  ☆59Updated 10 years ago
• AnyDSL / anyseq
  genome sequence alignment
  ☆14Updated 5 years ago
• dcjones / quip
  Compressing next-generation sequencing data with extreme prejudice.
  ☆80Updated 2 years ago
• nanoporetech / scrappie
  Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
  ☆93Updated 3 years ago
• NVIDIA-Genomics-Research / racon-gpu
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
  ☆16Updated 4 years ago
• ECP-CANDLE / Benchmarks
  ECP-CANDLE Benchmarks
  ☆59Updated 6 months ago
• CornellHPC / HySortK
  High Performance Sorting Based Distributed memory K-mer counter
  ☆12Updated 9 months ago
• gsneha26 / SegAlign
  A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
  ☆69Updated 7 months ago
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆166Updated last year
• ratschlab / graph_annotation
  Code accompanying the publication for compressed graph annotation
  ☆13Updated 6 years ago