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Top 8 k-mer open source projects

unikmer

Toolkit for k-mer with taxonomic information

✭ 46

go shell set union intersection kmer k-mer difference unique unik

kover

Learn interpretable computational phenotyping models from k-merized genomic data

✭ 47

python C++CMake machine-learning genomics k-mer phenotypes biomarker-discovery

iMOKA

interactive Multi Objective K-mer Analysis

✭ 19

javascript C++typescript HTML c python machine-learning gui angular singularity data-analysis k-mer rna-seq-analysis

ganon

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

✭ 57

python C++shell CMake bioinformatics bloom-filter metagenomics microbiome k-mer minimizers refseq-genbank

sshash

A compressed, associative, exact, and weighted dictionary for k-mers.

✭ 62

C++shell CMake hashing bioinformatics dictionary k-mer minimal-perfect-hash

charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

✭ 32

python Jupyter Notebook Standard ML bioinformatics metagenomics k-mer sourmash

kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

✭ 68

C++c bioinformatics genomics indexing k-mer sequence-similarity

raptor

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

✭ 37

C++CMake filter bloom-filter threshold binning k-mer minimizer set-membership

1-8 of 8 k-mer projects