CMU-SAFARI / RawHashLinks
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).
☆57Updated 6 months ago
Alternatives and similar repositories for RawHash
Users that are interested in RawHash are comparing it to the libraries listed below
Sorting:
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated 2 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Updated 2 years ago
- slow5lib is a software library for reading & writing SLOW5 files.☆46Updated 5 months ago
- Efficient low-divergence mapping of long reads in minimizer space☆67Updated last year
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆72Updated 10 months ago
- Assemblies from HPP Year 1 production☆76Updated 2 years ago
- a tool for simulating nanopore raw signal data☆66Updated 9 months ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆35Updated 2 months ago
- Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.☆99Updated last month
- Pangenome graphs (review article on graph-based pangenomic methods)☆72Updated 5 years ago
- GFA visualizer, GPU-accelerated using Vulkan☆71Updated 2 years ago
- PBSIM3: a simulator for all types of PacBio and ONT long reads☆78Updated 2 months ago
- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores☆72Updated last year
- Pan-Genomic Matching Statistics☆52Updated last year
- implicit pangenome graph☆61Updated this week
- 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
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆20Updated last month
- Scalable long read self-correction and assembly polishing with multiple sequence alignment☆55Updated last year
- ☆115Updated last year
- Visualise and analyse nanopore (ONT) raw signals☆117Updated this week
- ☆30Updated last year
- ☆12Updated 6 years ago
- Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing☆57Updated last year
- A streaming method for mapping nanopore raw signals☆32Updated 3 years ago
- PGR-TK: Pangenome Research Tool Kit☆100Updated last year
- MarginPolish: Graph based assembly polishing☆46Updated 4 years ago
- ClairS - a deep-learning method for long-read somatic small variant calling☆85Updated last month
- Predictive kmer models for development use☆58Updated 2 years ago
- lossless nanopore pod5 <=> s/blow5 file conversion☆40Updated 2 months ago
- ☆69Updated 5 months ago