CMU-SAFARI / RawHash
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).
☆52Updated 2 months ago
Alternatives and similar repositories for RawHash:
Users that are interested in RawHash are comparing it to the libraries listed below
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆42Updated last year
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores☆72Updated last year
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆67Updated 7 months ago
- a tool for simulating nanopore raw signal data☆66Updated 5 months ago
- Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.☆96Updated this week
- Assemblies from HPP Year 1 production☆73Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆19Updated last month
- The buttery eel - a slow5 guppy/dorado basecaller wrapper☆39Updated this week
- slow5lib is a software library for reading & writing SLOW5 files.☆42Updated last month
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆32Updated 5 months ago
- Pan-Genomic Matching Statistics☆50Updated 11 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 9 months ago
- GFA visualizer, GPU-accelerated using Vulkan☆70Updated 2 years ago
- Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads☆72Updated 5 months ago
- ☆12Updated 6 years ago
- Efficient low-divergence mapping of long reads in minimizer space☆65Updated last year
- Analysis pipelines from Oxford Nanopore Technologies' Research Division☆50Updated 4 years ago
- ClairS - a deep-learning method for long-read somatic small variant calling☆81Updated last week
- vcfdist: Accurately benchmarking phased variant calls☆79Updated 3 weeks ago
- ☆44Updated 2 months ago
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆33Updated 4 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆51Updated 9 months ago
- Computational pipeline for calling consensi on R2C2 nanopore data☆31Updated 3 years ago
- crab go snap snap☆37Updated last month
- Set of tools to manipulate and visualize modified base bam files☆52Updated 2 years ago
- Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing☆57Updated last year
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆48Updated 5 months ago
- PBSIM3: a simulator for all types of PacBio and ONT long reads☆71Updated 2 weeks ago
- Benchmarking pairwise aligners☆36Updated last month