fahaihi / SR2C
SR2C: A Novel Structurally Redundant Short Reads Collapser for Optimizing Genomic Sequencing Data Compression
☆9Updated last year
Alternatives and similar repositories for SR2C:
Users that are interested in SR2C are comparing it to the libraries listed below
- A Parallel Multi-FastQ-Files Reads Clustering Tool For Improving DNA Reads Compression☆17Updated last year
- A benchmark suite to study the performance characteristics of genomics applications☆29Updated 5 months ago
- A space-efficient compressor based on the Re-Pair grammar☆11Updated 7 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…☆55Updated 3 months ago
- Global alignment and alignment extension☆131Updated last year
- PPoPP24 AGAThA: Fast and Efficient GPU Acceleration of Guided Sequence Alignment for Long Read Mapping☆18Updated 10 months ago
- WFA-lib: Wavefront alignment algorithm library v2☆179Updated 2 weeks ago
- Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)☆47Updated last year
- Wavelet tree based on a fixed block boosting technique☆16Updated 3 years ago
- Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast See…☆11Updated 7 years ago
- A fuzzy Bruijn graph approach to long noisy reads assembly☆39Updated 8 years ago
- Inducing enhanced suffix arrays for string collections [DCC'16, TCS 2017]☆26Updated 2 years ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated last year
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆205Updated last month
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 5 years ago
- Compressor for Nanopore Sequencing Reads☆21Updated 2 years ago
- A cheatsheet for most common Stringology tasks☆15Updated 3 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆33Updated 6 months ago
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆16Updated 9 months 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
- Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays☆13Updated 2 weeks ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆29Updated 2 years ago
- gsufsort: building suffix arrays, LCP-arrays and BWTs for string collections [AMB 2020]☆27Updated last month
- ☆14Updated 4 months ago
- R-Index-F Library for Pattern Matching☆13Updated 7 months ago
- An optimal space run-length Burrows-Wheeler transform full-text index☆62Updated last year
- FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental r…☆107Updated 10 years ago
- High Performance Sorting Based Distributed memory K-mer counter☆12Updated 9 months ago
- online notebooks for a review of genome sketching☆61Updated 5 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆63Updated 9 months ago