kmer
There are 75 repositories under kmer topic.
jerryji1993/DNABERT
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
KamilSJaron/smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
shenwei356/kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
mcveanlab/mccortex
De novo genome assembly and multisample variant calling
tlemane/kmtricks
modular k-mer count matrix and Bloom filter construction for large read collections
shenwei356/unikmer
A versatile toolkit for k-mers with taxonomic information
zhangrengang/SubPhaser
To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
edawson/rkmh
Classify sequencing reads using MinHash.
OpenGene/UniqueKMER
Generate unique KMERs for every contig in a FASTA file
JensUweUlrich/Taxor
Fast and space-efficient taxonomic classification of long reads
jordanlab/stringMLST
Fast k-mer based tool for multi locus sequence typing (MLST)
andrewjpage/tiptoft
Predict plasmids from uncorrected long read data
suchapalaver/krust
Bioinformatics 101 tool for counting unique k-length substrings in DNA
alexpreynolds/kmer-counter
Count kmers with a more efficient (faster) hash table
edawson/mkmh
Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
jordanlab/STing
Ultrafast sequence typing and gene detection from NGS raw reads
nf-core/kmermaid
k-mer similarity analysis pipeline
slowikj/seqR
fast and comprehensive k-mer counting package
IQTLabs/freqgen
🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies
quwubin/paired-kmers
finding conserved regions in highly diverse genomes
brentp/nim-kmer
DNA kmer operations for nim
BioJulia/KmerAnalysis.jl
K-mer counting algorithms and count-data utilities for the BioJulia framework
AlgoLab/rs-vgaligner
Rust implementation of ekg's dozyg
AntonOresten/VectorizedKmers.jl
Fast K-mer counting in Julia
metageni/FOCUS
FOCUS: An Agile Profiler for Metagenomic Data
suchapalaver/fastas2kmers
A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.
TimRouze/supersampler
SuperSampler, an efficient scaled size sketching and sketch comparison tool
shenwei356/unik
A k-mer serialization package for Golang
wrf/lavaLampPlot
instructions, python and R code for generating lava lamp plots of kmer coverage
gi-bielefeld/pangrowth
Pangenome openness from k-mers or genes
alexpreynolds/kmer-collapse
Collapse a set of redundant kmers to use IUPAC degenerate bases
kcleal/kmerhash
Convert python string to hashed kmers and back again
Qile0317/KmerGMA.jl
A seed-based homology searching tool
shenwei356/go-hashing-kmer-bench
Benchmark of hashing k-mers in Golang