k-mer

There are 61 repositories under k-mer topic.

  • dib-lab/khmer

    In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

    Language:Python759681k295

  • bluenote-1577/sylph

    ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

    Language:Rust2013317

  • steineggerlab/Metabuli

    Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

    Language:C++12363710

  • lh3/yak

    Yet another k-mer analyzer

    Language:C1228249

  • mgalardini/pyseer

    SEER, reimplemented in python 🐍🔮

    Language:Python1131022227

  • bacpop/PopPUNK

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Language:Python94622220

  • pirovc/ganon

    ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

    Language:Python9247113

  • jermp/sshash

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

    Language:C++8552118

  • refresh-bio/kmer-db

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

    Language:C++8572617

  • shenwei356/unikmer

    A versatile toolkit for k-mers with taxonomic information

    Language:Go763237

  • bacpop/ska.rust

    Split k-mer analysis – version 2

    Language:Rust724405

  • dib-lab/charcoal

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

    Language:Python53191631

  • seqan/raptor

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

    Language:C++5245818

  • aldro61/kover

    Learn interpretable computational phenotyping models from k-merized genomic data

    Language:Python5175714

  • johnlees/seer

    sequence element (kmer) enrichment analysis

    Language:C++4377710

  • suchapalaver/krust

    Bioinformatics 101 tool for counting unique k-length substrings in DNA

    Language:Rust300185

  • Plant-Food-Research-Open/assemblyqc

    A Nextflow pipeline for evaluating assembly quality

    Language:Nextflow27131245
  • iMOKA

    RitchieLabIGH/iMOKA

    interactive Multi Objective K-mer Analysis

    Language:JavaScript233202

  • liaoherui/VirStrain

    An RNA virus strain-level identification tool for short reads.

    Language:Python203161

  • nf-core/kmermaid

    k-mer similarity analysis pipeline

    Language:Nextflow201433212

  • slowikj/seqR

    fast and comprehensive k-mer counting package

    Language:C++183471

  • mbhall88/skc

    Shared k-mer content between two genomes

    Language:Rust17100

  • deepomicslab/LocalHGT

    Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

    Language:Python13201

  • MatthewRalston/kmerdb

    Python bioinformatics CLI for k-mer counts and de Bruijn graphs

    Language:Python1221091
  • KEC

    berybox/KEC

    Unique sequence search by K-mer exclusion

    Language:Go8312

  • bioinfo-ut/AluMine

    Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes

    Language:Perl6212

  • luffy563/circRNA_tools_comparison

    This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.

    Language:Python6100

  • pmenzel/kiq

    K-mer indexing and querying in RNA-Seq data

    Language:C++6310

  • CamilaDuitama/decOM

    🗑️🦷 decOM 🦷🗑️

    Language:Python5422

  • tobiasrausch/rdxon

    Reference-free FASTQ filter for rare germline and somatic variants

    Language:C++530

  • akiomiyao/ped

    Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

    Language:Perl4302

  • BioGenies/CancerGram

    Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI.

    Language:R4300

  • CamilaDuitama/aKmerBroom

    🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

    Language:Python4102

  • zmmason/BINF

    Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

    Language:Python4100

  • pmenzel/biq

    Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets

    Language:JavaScript3200

  • shenwei356/go-hashing-kmer-bench

    Benchmark of hashing k-mers in Golang

    Language:Go3301