Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf
☆36Mar 29, 2020Updated 6 years ago
Alternatives and similar repositories for Shifted-Hamming-Distance
Users that are interested in Shifted-Hamming-Distance are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆11Dec 9, 2022Updated 3 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆19Jun 3, 2019Updated 7 years ago
- Lightweight String Graph Construction☆11May 10, 2023Updated 3 years ago
- find likely coding segments in DNA using composition-normalised hexamer tables☆18Oct 18, 2024Updated 2 years ago
- Utilities to detect and profile `het-kmers`☆12Aug 5, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast See…☆11Feb 5, 2018Updated 8 years ago
- a GFA toolkit☆13Oct 4, 2024Updated 2 years ago
- Sniphles is a read-based phasing approach for phased variant calling of structural variants.☆12Oct 14, 2020Updated 6 years ago
- de Bruijn Graph-based read aligner☆36Sep 3, 2018Updated 8 years ago
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆32Dec 19, 2022Updated 3 years ago
- the we-flyin WFA-guided ultralong tiling sequence aligner☆10May 13, 2021Updated 5 years ago
- Lightweight C++ library for reading FASTA and FASTQ files.☆12Feb 16, 2019Updated 7 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 3 years ago
- micro-read Fast Alignment Search Tool☆20Jul 19, 2019Updated 7 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 5 years ago
- efficient alignment of strings to partially ordered string graphs☆33Apr 22, 2026Updated 6 months ago
- ApHMM-GPU is the first GPU implementation of the Baum-Welch algorithm for profile Hidden Markov Models (pHMMs). It includes many of the s…☆11Jul 21, 2022Updated 4 years ago
- Global alignment and alignment extension☆144Jun 27, 2023Updated 3 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆23Mar 5, 2019Updated 7 years ago
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆57Mar 31, 2023Updated 3 years ago
- C implementation of the Landau-Vishkin algorithm☆36Apr 8, 2022Updated 4 years ago
- de Bruijn Graph-based read aligner☆11Jul 19, 2016Updated 10 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Aug 8, 2018Updated 8 years ago
- Rust bindings to the wavefront algorithm C implementation☆17Sep 20, 2022Updated 4 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆36Aug 4, 2021Updated 5 years ago
- Filter fasta/fastq(.gz) files by ID and/or sequence length☆14Feb 8, 2020Updated 6 years ago
- ☆16Jan 10, 2022Updated 4 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 9 years ago
- ☆14Jan 20, 2016Updated 10 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57May 29, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and comp…☆15Apr 6, 2022Updated 4 years ago
- Long read to reference genome mapping tool☆13Mar 14, 2024Updated 2 years ago
- Metasys is the first open-source FPGA-based infrastructure with a prototype in a RISC-V core, to enable the rapid implementation and eval…☆16Jan 20, 2023Updated 3 years ago
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆19Sep 4, 2024Updated 2 years ago
- This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye R…☆19May 21, 2017Updated 9 years ago
- SMASH is a hardware-software cooperative mechanism that enables highly-efficient indexing and storage of sparse matrices. The key idea of…☆19May 17, 2020Updated 6 years ago
- TransPimLib is a library for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, TransPimLib provides …☆15Apr 21, 2023Updated 3 years ago