k-mer

There are 4 repositories under k-mer topic.

dib-lab / khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python
Language:Python 738
lh3 / yak
Yet another k-mer analyzer
bioinformatics k-mer
Language:C 106
mgalardini / pyseer
SEER, reimplemented in python 🐍🔮
gwas bacteria k-mer reimplementation reproducible-science
Language:Python 96
bluenote-1577 / sylph
ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.
average-nucleotide-identity k-mer metagenomics sketching-algorithm taxonomic-classification
Language:Rust 93
bacpop / PopPUNK
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
bacteria genomics population-genetics k-mer sketching
Language:Python 79
jermp / sshash
A compressed, associative, exact, and weighted dictionary for k-mers.
hashing minimal-perfect-hash k-mer bioinformatics dictionary
Language:C++ 78
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
metagenomics bioinformatics k-mer bloom-filter microbiome minimizers taxonomy genbank gtdb ncbi refseq
Language:Python 78
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.).
bioinformatics genomics indexing k-mer sequence-similarity
Language:C++ 74
shenwei356 / unikmer
a versatile toolkit for k-mers with taxonomic information
kmer golang unique union intersection difference unik k-mer set
Language:Go 71
steineggerlab / Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
bioinformatics k-mer metagenomics taxonomic-classification taxonomy
Language:C++ 62
bacpop / ska.rust
Split k-mer analysis – version 2
bioinformatics sequence ska rust alignment k-mer
Language:Rust 54
aldro61 / kover
Learn interpretable computational phenotyping models from k-merized genomic data
machine-learning genomics k-mer biomarker-discovery phenotypes
Language:Python 50
seqan / raptor
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
minimizer k-mer binning threshold bloom-filter filter set-membership
Language:C++ 49
dib-lab / charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
bioinformatics metagenomics k-mer sourmash
Language:Python 48
johnlees / seer
sequence element (kmer) enrichment analysis
gwas bacteria k-mer
Language:C++ 41
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
iMOKA
RitchieLabIGH / iMOKA
interactive Multi Objective K-mer Analysis
singularity angular gui k-mer rna-seq-analysis data-analysis machine-learning
Language:JavaScript 23
nf-core / kmermaid
k-mer similarity analysis pipeline
nf-core workflow pipeline nextflow kmer k-mer kmer-frequency-count kmer-counting
Language:Nextflow 19
liaoherui / VirStrain
An RNA virus strain-level identification tool for short reads.
k-mer metagenomics reference-database strain virus
Language:Python 18
mbhall88 / skc
Shared k-mer content between two genomes
bioinformatics k-mer
Language:Rust 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
MatthewRalston / kmerdb
Python bioinformatics CLI for k-mer counts and de Bruijn graphs
bgzf bioinformatics k-mer k-mer-counting k-mer-frequency k-mer-hashing python-cli
Language:Python 12
KEC
berybox / KEC
Unique sequence search by K-mer exclusion
bioinformatics detection genome genome-analysis genomics k-mer
Language:Go 8
deepomicslab / LocalHGT
Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.
hgt k-mer metagenomics strain bacterial-genome-analysis microbiome horizental-gene-transfer mobile-gene-element structual-variation
Language:Python 8
luffy563 / circRNA_tools_comparison
This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.
bioinformatics circrna comparison-benchmarks algorithms k-mer reads-mapping
Language:Python 6
bioinfo-ut / AluMine
Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes
genomics alignment-free-algorithm k-mer transposable-element alu repeatmasker
Language:Perl 5
pmenzel / kiq
K-mer indexing and querying in RNA-Seq data
transcriptomics k-mer rna-seq k-mer-counting
Language:C++ 5
tobiasrausch / rdxon
Reference-free FASTQ filter for rare germline and somatic variants
rare-disease cancer-genomics sequencing k-mer reference-free pan-genome variant-calling
Language:C++ 5
akiomiyao / ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
polymorphism inversion insertion ngs deletion snp k-mer ngstools alignment-free-algorithm somatic-mutations genotype sequence-alignments variant cnv copy-number-variation crispr-cas9
Language:Perl 4
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.
anticancer-peptides bioinformatics k-mer n-gram peptide-identification r-package random-forests
Language:R 4
CamilaDuitama / decOM
🗑️🦷 decOM 🦷🗑️
contamination k-mer matrix ancient-dna calculus bioinformatics
Language:Python 4
zmmason / BINF
Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.
orf cyclic-pattern mass-spectrometry genome-analysis fasta fasta-sequences peptides cyclic-peptides dna motif directed-acyclic-graph de-bruijn-graphs overlap-graph protein-sequence k-mer z-score markov-chain
Language:Python 4
CamilaDuitama / aKmerBroom
🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
adna decontamination k-mer bloomfilter metagenomics dentalcalculus ancientdna
Language:Python 3
MislavJaksic / Bioinformatics-Finding-Mutations
Assembles a genome and finds true mutations among sequencing errors
bioinformatics k-mer minimizer alignment mutations c-plus-plus
Language:C++ 3
pmenzel / biq
Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets
circrna k-mer transcriptomics circular-rna sra rna-seq backsplice-junction
Language:JavaScript 3
md5sam / aKmerBroom
🧹 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
ancient-dna bioinformatics bloom-filter k-mer
Language:Python 2

k-mer

dib-lab / khmer

lh3 / yak

mgalardini / pyseer

bluenote-1577 / sylph

bacpop / PopPUNK

jermp / sshash

pirovc / ganon

refresh-bio / kmer-db

shenwei356 / unikmer

steineggerlab / Metabuli

bacpop / ska.rust

aldro61 / kover

seqan / raptor

dib-lab / charcoal

johnlees / seer

suchapalaver / krust

RitchieLabIGH / iMOKA

nf-core / kmermaid

liaoherui / VirStrain

mbhall88 / skc

slowikj / seqR

MatthewRalston / kmerdb

berybox / KEC

deepomicslab / LocalHGT

luffy563 / circRNA_tools_comparison

bioinfo-ut / AluMine

pmenzel / kiq

tobiasrausch / rdxon

akiomiyao / ped

BioGenies / CancerGram

CamilaDuitama / decOM

zmmason / BINF

CamilaDuitama / aKmerBroom

MislavJaksic / Bioinformatics-Finding-Mutations

pmenzel / biq

md5sam / aKmerBroom