kmer-frequency-count

There are 1 repository under kmer-frequency-count topic.

• nf-core / kmermaid

  k-mer similarity analysis pipeline

  nf-coreworkflowpipelinenextflowkmerk-merkmer-frequency-countkmer-counting
  Language:Nextflow 19

• pnnl / mercat

  MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

  metagenomic-analysismetatranscriptomic-analysiskmer-frequency-countplotlydiversitydivideandconquerpythondaskk-mer-countingk-mer-frequencyproteinnucleotidesfastqdiversity-estimationdatabase-independent-analysis
  Language:Python 18
• Discount

  jtnystrom / Discount

  Very large scale k-mer counting and analysis on Apache Spark.

  bioinformaticsgenomicskmer-countingkmer-frequency-countkmersscalaspark
  Language:Scala 17

• slowikj / seqR

  fast and comprehensive k-mer counting package

  k-mer-countingkmerkmer-countingkmer-frequency-countkmersngramsngramrcpprcppparallelrpackagebioinformaticsbioinformatics-toolgenomicsprotein-sequenceshashingfeature-engineeringfeature-extractiondna-processingk-merhashing-algorithms
  Language:C++ 16

• BioJulia / KmerAnalysis.jl

  K-mer counting algorithms and count-data utilities for the BioJulia framework

  biojuliakmerkmer-compositionkmer-countingkmer-distributionkmer-frequency-countkmer-spectrakmers
  Language:Julia 12

• raw-lab / mercat2

  MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

  pythondiversityplotlymultiomicsmultiomics-dataproteindaskfastqk-mer-countingk-mer-frequencydivideandconquermetagenomic-analysismetatranscriptomic-analysiskmer-frequency-countnucleotidesdiversity-estimationdatabase-independent-analysis
  Language:HTML 11

• 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.

  kmerkmer-countingkmer-frequency-countkmerskmer-lengthfasta-sequencesfasta-format
  Language:Python 9

• anuradhawick / kmertools

  kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more

  bioinformaticskmer-compositionkmer-countingkmer-frequency-countmetagenomics
  Language:Rust 6

• sanger-tol / sequencecomposition

  Nextflow pipeline to extract statistics from a genome about its sequence composition

  genomicsnextflowpipelinekmer-frequency-countrunning-averageshannon-entropy
  Language:Groovy 2

• alexpreynolds / kmer-counter-abseil

  Count canonical kmers with Abseil C++ `absl::flat_hash_map`

  cpphash-tablesbioinformaticskmer-countingkmer-frequency-countkmerbazelbazel-examplesabseil
  Language:C++ 1

• Selvalakshmi27 / Kspectra

  Generate K-mer spectra to observe modalities of distributions

  kmer-distributionkmer-frequency-countkmers
  Language:Python 1

• ShawnMOlichwier / KmerResearch

  Kmer Research in Python and R

  kmer-frequency-countmachine-learningbioinformatics
  Language:R 1

• bissim / bgp-d2

  This is our implementation for D2 distance algorithm for k-mers.

  bioinformaticskmerkmer-frequency-countkmerskmer-distribution
  Language:Java 0

• rejoyc-cs / k_mer_in_DNA

  Counts the number of occurrences of each k-mer in a DNA string

  biologycomputational-biologydnadna-sequenceskmer-countingkmer-frequency-countmatplotlibmicrobiologyprogrammingpython
  Language:Python 0

• smhuprikar / AdapterFinder

  A program to read sequences from fastq file and find out the frequency of all substrings with length k across all sequences in the file.

  kmerkmer-frequency-countfastq-filesfastqkmer-counting
  Language:Python 0

• urmilkadakia / ParallelKmerEstimate

  A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage in Parallel

  kmerkmer-frequency-count
  Language:C++ 0

• alexpreynolds / kmer-counter-boost

  Count canonical kmers with Boost C++ `boost::unordered_map` hash table

  cpphash-tablesbioinformaticskmer-frequency-countkmer-countingkmerbazelbazel-examplesboost
  Language:C++

• alexpreynolds / kmer-counter-emilib

  Count canonical kmers with Emil Ernerfeldt's emilib::HashMap

  cpphash-tablesbioinformaticskmer-frequency-countkmer-countingkmer
  Language:C++

• alexpreynolds / kmer-counter-ska

  Count canonical kmers with Malte Skarupke's bytell_hash_map hash table

  cpphash-tablesbioinformaticskmer-frequency-countkmer-countingkmer
  Language:C++

• alexpreynolds / kmer-counter-sparse

  Count canonical kmers with Google sparse_hash_map

  cpphash-tablesbioinformaticskmer-frequency-countkmer-countingkmer
  Language:C++

• alexpreynolds / kmer-counter-unordmap

  Count canonical kmers with STL unordered_map

  cpphash-tablesbioinformaticskmer-frequency-countkmer-countingkmer
  Language:C++

• gauravcodepro / kmerstring-count-graph

  a ruby function for kmer iterations and kmer graph preparation. estimates the kmers and gives occurrences as tab delimited

  graphkmer-compositionkmer-countingkmer-frequency-countrubystring-matchingrubypr
  Language:Ruby

• turkdogan / kmer-counter

  Counts k-kmers and sorts top "k" kmer by occurrence.

  cppkmerkmer-frequency-countbloom-filter
  Language:C++