yaobaiwei / PPA-Assembler
A toolkit for de novo genome assembly based on Pregel.
☆12Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for PPA-Assembler
- A fuzzy Bruijn graph approach to long noisy reads assembly☆39Updated 7 years ago
- High Performance Sorting Based Distributed memory K-mer counter☆11Updated 4 months ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆27Updated 2 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆48Updated 2 years ago
- Parallel k-mer indexing for biological sequences☆12Updated 5 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆16Updated 5 years ago
- A more efficient quality control tool for sequencing data☆22Updated 2 weeks ago
- ☆8Updated 2 years ago
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆15Updated 5 months ago
- Pacbio sequence alignment tool, please use "git clone" to copy and use the repository☆18Updated 5 years ago
- Efficient construction of the BWT using string compression☆17Updated last month
- ☆15Updated 5 months ago
- Rust crate with bindings and interface to the SPOA library for generating consensus sequences.☆10Updated 5 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 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 tool for merging large BWTs☆26Updated 3 years ago
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆23Updated 3 months ago
- RabbitMash: an efficient highly optimized implementation of Mash.☆21Updated last year
- ☆12Updated 5 years ago
- Fast and accurate set similarity estimation via containment min hash☆42Updated 4 months ago
- ☆17Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆18Updated last month
- Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)☆45Updated 8 months ago
- Ultra fast MSD radix sorter☆11Updated 4 years ago
- Validation of sycnmers compared to minimizers☆11Updated 4 years ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆22Updated 2 weeks ago
- Long Approximate Matches-based Split Aligner☆13Updated 7 years ago
- Implementation of a Backpack Quotient Filter☆10Updated 4 months ago
- FMtree: A fast locating algorithm of FM-indexes for genomic data☆18Updated 7 years ago