kmers

There are 0 repository under kmers topic.

jermp / fulgor
Fulgor is a fast and space-efficient colored de Bruijn graph index.
bioinformatics de-bruijn-graphs hashing kmers
Language:C++ 32
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
akcorut / kGWASflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
snakemake genomics gwas gwas-pipeline kmers bioinformatics-pipeline ngs sciworkflows bioinformatics conda pipeline association-mapping bioinformatics-tool gwas-tools structural-variation workflow
Language:Python 25
Discount
jtnystrom / Discount
Very large scale k-mer counting and analysis on Apache Spark.
spark scala kmer-counting kmer-frequency-count kmers bioinformatics genomics
Language:Scala 17
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
arminZolfaghari / DNA-Sequence-Classification
Analysis of DNA Sequence Classification Using Neural Networks - Bioinformatics Course Project - Winter 2022
classification deep-learning dna dna-sequence-analysis kmers word-embedding bioinformatics dna-analysis
Language:Jupyter Notebook 13
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
OndrejSladky / kmercamel
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
bioinformatics bioinformatics-tool genomics k-mers kmers masked-superstrings
Language:C++ 11
dib-lab / kmerDecoder
Extract kmers, skipmers, minimizers.
kmers skipmers skip-mers minimizers
Language:C++ 10
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 10
bioinfoUQAM / CASTOR_KRFE
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
alignment-free castor castor-krfe feature-extraction kmers machine-learning rfe svm svm-rfe taxonomic-classification virus-classification
Language:Python 9
hannesbecher / shiny-k-mers
Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
k-mers k-mer-spectrum allotetraploidy genome-size polyploidy kmers tetmer bioinformatics ploidy-inference
Language:R 9
phylo42 / RAPPAS
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
placement phylogenetic-placement metagenomics metabarcoding phylogenetics genetic-markers kmers phylo-kmers taxonomic-classification
Language:Java 9
phylo42 / sherpas
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences
virus recombination subtyping genotyping kmers phylo-kmers recombination-detection ancestral-sequences
Language:C++ 8
shenwei356 / kmers
bit-packed k-mers methods for Golang
kmers bit-pack
Language:Go 8
moorembioinfo / KmerAperture
Extract SNPs and accessory differences in closely related bacterial genomes from k-mers
alignment-free genomics kmers snps
Language:Python 6
GioStamoulos / Kmers_Dataset_Generation_Regression_Clustering
The generation of a kmers dataset that is associated with multiple gene sequences and the further manipulation of this generated dataset are the main contents of the current project.
bioinformatics blast genomics kmers regression clustering svr kmeans isomap pandas sklearn matplotlib machine-learning data-harvesting data-manipulation computational-biology
Language:Jupyter Notebook 3
adamjorr / kbbq
reference-free base quality score recalibration
bioinformatics kmers genomics fastq htslib
Language:C++ 2
kcleal / kmerhash
Convert python string to hashed kmers and back again
bioinformatics hash kmer kmers
Language:Cython 2
gabrielecanesi / DNA-SNP-finder
An algorithm for finding SNPs of a long read compared to a reference genome
bioinformatics dna-sequences kmers spaced-seed
Language:C++ 1
Gulshan-gaur / NAUniSeq
NAUniSeq: A fast computational pipeline to search unique sequences for microbial diagnostics
amino-acid-sequence bioinformatics dna kmers microbial-genomics ncbi-taxonomy
Language:Python 1
maremita / slm_kgenomvir
Evaluation of Statistical Linear Models for Genome Virus Classification
bayesian machine-learning markov-chain-model taxonomic-classification virus-classification statistical-linear-models kmers
Language:Jupyter Notebook 1
polyglotDataNerd / poly-spark-kmers
spark scala bioinformatics kmers
Language:Scala 1
Selvalakshmi27 / Kspectra
Generate K-mer spectra to observe modalities of distributions
kmer-distribution kmer-frequency-count kmers
Language:Python 1
andriusbern / afp
Alignment-Free phylogenetic tree construction from .fasta sequence files
alignment-free-algorithm fasta kmers
Language:C++ 0
bissim / bgp-d2
This is our implementation for D2 distance algorithm for k-mers.
bioinformatics kmer kmer-distribution kmer-frequency-count kmers
Language:Java 0
maremita / CASTOR_KRFE_v1.0
[Features extraction method] You can find the new version of CASTOR_KRFE at https://github.com/bioinfoUQAM/CASTOR_KRFE
alignment-free kmers rfe taxonomic-classification virus-classification kmer-extraction castor svm svm-rfe castor-krfe
Language:Python 0
panthijeeban / Python-Assignment
Python assignment for my Bio-535 course at URI, Spring 2018.
dna fasta genetics graphs kmers python sequence
Language:Python 0
rupeshsure / DNA-Sequence-Classification-Project
DNA CLASSIFICATION
dna-sequences countvectorizer dna-sequencing hyperparameter-optimization kmeans-clustering machine-learning machine-learning-algorithms nlp-machine-learning transform bagofwords kmers multiclass-classification supervised-machine-learning
Language:Jupyter Notebook 0
victoria-r / BioPython
A collection of various biopython scripts.
bioinformatics biopython fasta genbank kmers orfs python3 transcription translation
Language:Python 0
jermp / fulgor-benchmarks
Benchmarks and evaluation scripts for the Fulgor index.
bioinformatics de-bruijn-graphs hashing kmers
Language:Python
kalyaniasthana / FindingHiddenMessagesInDNA_BioinformaticsI
Coding problems from course 1 of the Bioinformatics specialization
bioinformatics algorithms randomized-algorithms motif-finding kmers bioinformatics-algorithms
Language:Python
Louis-MG / META-DIFF
This is the repository of the pipeline META-DIFF, which detects sequences in differential abundances between two conditions, and annotates them taxonomicaly and functionaly.
annotation bioinformatics-pipeline kmers metagenomics shotgun-pipeline snakemake
Language:R