edawson / rkmhView external linksLinks
Classify sequencing reads using MinHash.
☆48Apr 6, 2020Updated 5 years ago
Alternatives and similar repositories for rkmh
Users that are interested in rkmh are comparing it to the libraries listed below
Sorting:
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Jul 12, 2021Updated 4 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 10 months ago
- Pan-Genomic Matching Statistics☆55Apr 3, 2024Updated last year
- Parallel Sequence to Graph Alignment☆36Nov 26, 2022Updated 3 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65May 11, 2020Updated 5 years ago
- ☆13Jan 20, 2016Updated 10 years ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 4 years ago
- De novo genome assembly and multisample variant calling☆112Mar 28, 2019Updated 6 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 2 months ago
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 3 months ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 5 months ago
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆97May 20, 2025Updated 8 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- Fast genome and metagenome distance estimation using MinHash☆434Sep 19, 2025Updated 4 months ago
- Long read to reference genome mapping tool☆13Mar 14, 2024Updated last year
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated last year
- ☆24Aug 25, 2025Updated 5 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆24Jan 6, 2026Updated last month
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Blast2Bam uses the XML results of Blastn, the reference and the fastQ or fasta file(s) to output a SAM file.☆49May 25, 2021Updated 4 years ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- C++ library for analysing and storing large-scale cohorts of sequence variant data☆17Aug 27, 2019Updated 6 years ago
- Standalone C library for assembling Illumina short reads in small regions☆72Dec 15, 2022Updated 3 years ago
- Reference-free variant discovery in large eukaryotic genomes☆42Jul 13, 2021Updated 4 years ago
- 📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.☆93Updated this week
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆274Oct 13, 2022Updated 3 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- Predict plasmids from uncorrected long read data☆41Oct 31, 2025Updated 3 months ago
- Minimum Bait Cover Toolkit Syotti.☆13Jan 22, 2025Updated last year
- ☆84Sep 13, 2023Updated 2 years ago
- Histosketching Using Little Kmers☆56May 25, 2023Updated 2 years ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆31Jan 19, 2021Updated 5 years ago
- A tool for removing redundant genomes from a set of assemblies☆78Sep 10, 2025Updated 5 months ago
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 7 years ago
- This repo is DEPRECATED. Please use minimap2, the successor of minimap.☆106Sep 20, 2017Updated 8 years ago