kmer

There are 1 repository under kmer topic.

jerryji1993 / DNABERT
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
deep-learning dnabert-model genome gpu kmer kmer-format machine-learning natural-language-processing nlp sequence
Language:Python 536
sourmash
sourmash-bio / sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling
Language:Python 431
smudgeplot
KamilSJaron / smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
genomics bioinformatics kmer
Language:R 213
kmcp
shenwei356 / kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
kmer sketch searching metagenomics taxonomic-classification taxonomic-profiling scaled-minhash syncmers cobs sketching bigsi fracminhash virome
Language:Go 170
mcveanlab / mccortex
De novo genome assembly and multisample variant calling
genome-assembly de-bruijn-graphs kmer cortex variant-calling genome-graph contigs genome-analysis genomics
Language:C 110
shenwei356 / unikmer
a versatile toolkit for k-mers with taxonomic information
kmer golang unique union intersection difference unik k-mer set
Language:Go 70
tlemane / kmtricks
modular k-mer count matrix and Bloom filter construction for large read collections
kmer count matrix bloom-filters
Language:C++ 66
edawson / rkmh
Classify sequencing reads using MinHash.
nanopore minhash mutations openmp bioinformatics kmer
Language:C++ 47
zhangrengang / SubPhaser
Phase, partition and visualize subgenomes of an allopolyploid or hybrid based on the subgenome-specific repetitive kmers.
allopolyploid subgenome kmer partition phasing exchange
Language:Python 45
jordanlab / stringMLST
Fast k-mer based tool for multi locus sequence typing (MLST)
python mlst bacterial-genomes bacterial-database bioinformatics fastq-files kmer applied-bioinformatics-lab
Language:Python 41
OpenGene / UniqueKMER
Generate unique KMERs for every contig in a FASTA file
unique kmer sequencing bioinformatics ngs virus fasta
Language:C 41
andrewjpage / tiptoft
Predict plasmids from uncorrected long read data
genomics oxford-nanopore nanopore plasmid pacbio uncorrected research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen long-reads kmer plasmidfinder
Language:Python 37
suchapalaver / krust
counts k-mers, written in rust
kmer kmer-counting k-mer k-mers k-mer-counting kmers rust rust-bio rayon dashmap bioinformatics bioinformatics-tool bitpacking parallelization beginner-friendly needletail bytes clap insta genomics
Language:Rust 29
alexpreynolds / kmer-counter
Count kmers with a more efficient (faster) hash table
kmer genomics cpp14 bioinformatics hash-map kmer-counting
Language:C++ 24
edawson / mkmh
Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
minhash kmer locality-sensitive-hashing
Language:C++ 23
STing
jordanlab / STing
Ultrafast sequence typing and gene detection from NGS raw reads
mlst cgmlst kmer cpp genomics computational-biology ngs ngs-analysis genes databases dna
Language:C++ 19
nf-core / kmermaid
k-mer similarity analysis pipeline
nf-core workflow pipeline nextflow kmer k-mer kmer-frequency-count kmer-counting
Language:Nextflow 19
IQTLabs / freqgen
🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies
kmer genetic-algorithm codon-usage fasta
Language:Python 16
JensUweUlrich / Taxor
Fast and space-efficient taxonomic classification of long reads
kmer long-read long-read-sequencing metagenomics syncmer taxonomic-classification taxonomic-profiling bioinf em-algorithm pseudo-alignment xor-filter interleaved-xor-filter bioinformatics microbiome refseq taxonomy
Language:C++ 15
slowikj / seqR
fast and comprehensive k-mer counting package
k-mer-counting kmer kmer-counting kmer-frequency-count kmers ngrams ngram rcpp rcppparallel rpackage bioinformatics bioinformatics-tool genomics protein-sequences hashing feature-engineering feature-extraction dna-processing k-mer hashing-algorithms
Language:C++ 15
brentp / nim-kmer
DNA kmer operations for nim
nim-lang kmer genomics
Language:Nim 14
quwubin / paired-kmers
finding conserved regions in highly diverse genomes
design pcr primer bacterial kmer virus
Language:Go 14
BioJulia / KmerAnalysis.jl
K-mer counting algorithms and count-data utilities for the BioJulia framework
biojulia kmer kmer-counting kmer-distribution kmer-frequency-count kmer-composition kmers kmer-spectra
Language:Julia 12
AlgoLab / rs-vgaligner
Rust implementation of ekg's dozyg
rust alignment chaining anchors poa bioinformatics kmer
Language:Rust 9
anton083 / VectorizedKmers.jl
Efficient K-mer counting in Julia
dna kmer sequence
Language:Julia 9
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.
kmer kmer-counting kmer-frequency-count kmers kmer-length fasta-sequences fasta-format
Language:Python 8
TimRouze / supersampler
SuperSampler, an efficient scaled size sketching and sketch comparison tool
bioinformatics kmer sequence-analysis sketching
Language:C++ 8
metageni / FOCUS
FOCUS: An Agile Profiler for Metagenomic Data
metagenomes kmer identify-organisms bioinformatics microbiome
Language:Python 7
shenwei356 / unik
A k-mer serialization package for Golang
kmer kmer-file serialization taxid
Language:Go 7
wrf / lavaLampPlot
instructions, python and R code for generating lava lamp plots of kmer coverage
genomics metagenomics visualization rshiny kmer lavalampplot quality-control
Language:Python 6
lzhLab / kmcEx
ngs kmer encoding-kmers
Language:C++ 4
alexpreynolds / kmer-collapse
Collapse a set of redundant kmers to use IUPAC degenerate bases
bioinformatics kmer iupac encoding
Language:Python 3
jlanga / exfi
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
transcriptomics rna-seq assembly kmer bloom-filter abyss bedtools python3 conda bioconda biobloomtools exon transcriptome abyss-bloom biopython pandas network splice-graphs
Language:Python 3
mooreryan / eigengenomes
A C and Python implementation of latent strain analysis for eigengenome partitioning.
bioinformatics metagenomics clustering partitioning assembly kmer hyperplane
Language:C 3
KmerGMA.jl
Qile0317 / KmerGMA.jl
A kmer-based homology searching tool
genomics kmer kmer-counting bioinformatics homology homology-search
Language:Julia 2
slw287r / kmsk
Mask homologous sequences in query fasta(s) by kmers of subject fasta
host kmer mask mngs
Language:C 2