edawson / mkmh
Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
☆24Updated 4 years ago
Alternatives and similar repositories for mkmh:
Users that are interested in mkmh are comparing it to the libraries listed below
- A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)☆14Updated 3 years ago
- Classify sequencing reads using MinHash.☆48Updated 4 years ago
- reference free variant assembly☆32Updated last year
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆26Updated last year
- nimble aligner that will map your reads to the references on a laptop☆12Updated 7 years ago
- ☆14Updated 8 years ago
- drunk on perbase pileups and lua expressions☆17Updated last year
- Linear-time, low-memory construction of variation graphs☆18Updated 4 years ago
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆14Updated last year
- Bam Read Index - Extract alignments from a bam file by readname☆24Updated 8 months ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Updated 2 years ago
- Hidden Markov Model based Copy number caller☆20Updated 2 months ago
- Minimizer-based assembly scaffolding and mapping using long reads☆34Updated 3 months ago
- Index and query k-mer matrices in BGZF☆12Updated 6 years ago
- Python bindings to minimap2☆16Updated 7 years ago
- ☆22Updated last month
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆11Updated 10 months ago
- Variant call adjudication☆16Updated 7 months ago
- This repo is deprecated. Please use gfatools instead.☆16Updated 6 years ago
- Using reference-free compressed data structures to analyse thousands of human genomes (1000 Genomes ReadServer)☆14Updated 7 years ago
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Updated 3 years ago
- ☆12Updated 3 years ago
- Indel-aware consensus for aligned BAM☆21Updated last month
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Updated 5 years ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆22Updated last year
- Filter of Pairwise Alignement☆44Updated 2 years ago
- An experimental tool to find approximate max-cuts in a large graph☆11Updated 3 years ago
- For bluntifying overlapped GFAs☆13Updated 5 months ago
- Scalable and High Performance Variant Calling on Cluster Environments☆10Updated 2 years ago