dkoslicki / CMash
Fast and accurate set similarity estimation via containment min hash
☆42Updated 6 months ago
Alternatives and similar repositories for CMash:
Users that are interested in CMash are comparing it to the libraries listed below
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆33Updated last year
- Code to create a PRG from a Multiple Sequence Alignment file☆22Updated 9 months ago
- ☆12Updated 5 years ago
- Library of sketching functions used by PopPUNK☆30Updated last week
- de Bruijn Graph-based read aligner☆33Updated 6 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
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆46Updated this week
- This repo is deprecated. Please use gfatools instead.☆16Updated 6 years ago
- A k-mer search engine for all Sequence Read Archive public accessions☆19Updated 2 months ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- A lightweight library for working with PAF (Pairwise mApping Format) files☆31Updated 2 years ago
- extract MSAs from genome variation graphs☆33Updated 4 years ago
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- Parallel Sequence to Graph Alignment☆35Updated 2 years ago
- deSAMBA: fast and accurate classification of metagenomics long reads with sparse approximate matches☆10Updated 8 months ago
- Haplotype-aware genome assembly toolkit☆29Updated 5 years ago
- RabbitMash: an efficient highly optimized implementation of Mash.☆21Updated last year
- Tool to estimate deltas for sequence sets and answer questions about relative contribution☆21Updated this week
- Paired reads mapping on de Bruijn graph☆13Updated 6 years ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆21Updated this week
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆58Updated 9 months ago
- Iterate over minimizers of a DNA sequence☆27Updated 6 months ago
- REINDEER REad Index for abuNDancE quERy☆57Updated 5 months ago
- URMAP ultra-fast read mapper☆38Updated 4 years ago
- Johns Hopkins University student-led genomics paper discussion group☆13Updated 4 years ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆27Updated 9 months ago
- A FASTA/FASTQ format parser library☆20Updated 10 months ago
- d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly☆19Updated 6 years ago
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆16Updated 5 years ago