laurentnoe/iedera

subset and spaced seed design tool

Language: C++ - Size: 1.26 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 1

jermp/sshash

📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.

Language: C++ - Size: 24.7 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 84 - Forks: 18

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++ - Size: 5.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 89 - Forks: 18

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Language: Perl - Size: 12.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 4 - Forks: 2

seqan/raptor

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

Language: C++ - Size: 4.32 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 52 - Forks: 18

Sh1ne111/KMERIA

A KMER-based genome-wIde Assocation testing approach on polyploids

Language: C - Size: 16.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 0

steineggerlab/Metabuli

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

Language: C++ - Size: 92.3 MB - Last synced at: 5 days ago - Pushed at: 10 days ago - Stars: 139 - Forks: 12

bacpop/sketchlib.rust

Fast sequence distance estimates

Language: Rust - Size: 5.07 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 2

bacpop/ska.rust

Split k-mer analysis – version 2

Language: Rust - Size: 716 KB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 85 - Forks: 6

dib-lab/khmer

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

Language: Python - Size: 50.4 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 769 - Forks: 297

snipe-bio/snipe

Blazingly fast SRA-scale sequence analysis & QC

Language: Python - Size: 2.83 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

JNP-Solutions/Slacken

Highly scalable implementation of the Kraken 2 genomic sequence classification method. Based on Apache Spark.

Language: Scala - Size: 107 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

WCSCourses/K-mer_Biodiversity_Genomics_2025

Introduction and advanced uses of k-mers in biodiversity genomics using modern k-mer tools and methods.

Size: 23.4 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 3 - Forks: 0

ElenaBiagi/Finito

Here we introduce frequency-bounded minimizers - finimizers - for indexing sets of k-mers.

Language: C++ - Size: 389 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 9 - Forks: 1

lh3/yak

Yet another k-mer analyzer

Language: C - Size: 85.9 KB - Last synced at: 17 days ago - Pushed at: about 1 year ago - Stars: 133 - Forks: 9

nf-core/kmermaid

k-mer similarity analysis pipeline

Language: Nextflow - Size: 12.8 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 21 - Forks: 13

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: Python - Size: 24.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 96 - Forks: 12

mgalardini/pyseer

SEER, reimplemented in python 🐍🔮

Language: Python - Size: 73.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 121 - Forks: 27

MatthewRalston/kmerdb

Python CLI

Language: Python - Size: 59.2 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 1

liaoherui/VirStrain

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

Language: Python - Size: 6.83 MB - Last synced at: 5 days ago - Pushed at: 12 months ago - Stars: 21 - Forks: 1

Morteza1814/PARMIK

PARMIK is a fast and memory-efficient tool for identifying the "Partial Match" region between two genomic sequences.

Language: C++ - Size: 274 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 1

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

Language: Nextflow - Size: 63.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 33 - Forks: 7

bluenote-1577/sylph

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

Language: Rust - Size: 27.6 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 214 - Forks: 8

bacpop/PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Language: Python - Size: 116 MB - Last synced at: 18 days ago - Pushed at: 2 months ago - Stars: 97 - Forks: 20

johnlees/seer

sequence element (kmer) enrichment analysis

Language: C++ - Size: 1.32 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 43 - Forks: 10

shenwei356/unikmer

A versatile toolkit for k-mers with taxonomic information

Language: Go - Size: 6.18 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 77 - Forks: 7

rarissimaavis/bfcounter-bloom-filter

Analisi di un tool per il conteggio dei k-mer tramite Bloom Filter

Size: 3.29 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

romanyn36/DNA-searching-algorithms-pyqt6

simple desktop app that apply some of DNA searching algorithms, with easy use desktop GUI using Pyqt6 lib in python.

Language: Python - Size: 1.75 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

slowikj/seqR

fast and comprehensive k-mer counting package

Language: C++ - Size: 1.72 MB - Last synced at: 8 days ago - Pushed at: over 3 years ago - Stars: 18 - Forks: 1

BioGenies/kmerFilters

Tools for filtering k-mer data

Language: R - Size: 1.09 MB - Last synced at: 6 days ago - Pushed at: 8 months ago - Stars: 0 - Forks: 1

suchapalaver/krust

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

Language: Rust - Size: 23.1 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 30 - Forks: 5

deepomicslab/LocalHGT

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

Language: Python - Size: 65.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 10 - Forks: 1

seqan/minions

Comparison between different methods to simplify sequence data

Language: C++ - Size: 12.2 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 2

tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

Language: C++ - Size: 89.8 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 0

CamilaDuitama/decOM

🗑️🦷 decOM 🦷🗑️

Language: Python - Size: 203 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 2

CamilaDuitama/aKmerBroom

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

Language: Python - Size: 6.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

Chemical118/TRIS

Telomeric Repeat motif Identification tool with Short-read sequencing

Language: C++ - Size: 43.9 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

ryought/dbgphmm

Probabilistic genome assembler based on de Bruijn Graph and profile HMM

Language: Rust - Size: 2.13 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

bioinfo-ut/AluMine

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

Language: Perl - Size: 932 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

berybox/KEC

Unique sequence search by K-mer exclusion

Language: Go - Size: 5.53 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 2

dib-lab/charcoal

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

Language: Python - Size: 19.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 43 - Forks: 1

mbhall88/skc

Shared k-mer content between two genomes

Language: Rust - Size: 33.2 KB - Last synced at: 1 day ago - Pushed at: almost 2 years ago - Stars: 17 - Forks: 0

benvenutti/ganon Fork of pirovc/ganon

A read classification tool based on Interleaved Bloom Filters

Language: Python - Size: 11.2 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

Zheludev/KmerCatcher

A simple python script that counts k-mer matches between reference database and query .fasta files, optionally returning all non-matching query sequences. Designed originally for sequencing adapter decontamination.

Language: Python - Size: 21.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

aldro61/kover

Learn interpretable computational phenotyping models from k-merized genomic data

Language: Python - Size: 4.38 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 50 - Forks: 16

mhyfritz/k-mers

Enumerate k-mers of a given string.

Language: JavaScript - Size: 66.4 KB - Last synced at: 6 days ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

shenwei356/simhash-eval

Language: Go - Size: 2.91 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

shenwei356/go-hashing-kmer-bench

Benchmark of hashing k-mers in Golang

Language: Go - Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

md5sam/aKmerBroom

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

Language: Python - Size: 6.7 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

pmenzel/kiq

K-mer indexing and querying in RNA-Seq data

Language: C++ - Size: 77.1 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

Scien-ide/Helix 📦

A PHP hash table optimized for counting short gene sequences for use in Bioinformatics.

Language: PHP - Size: 227 KB - Last synced at: 27 days ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

RitchieLabIGH/iMOKA

interactive Multi Objective K-mer Analysis

Language: JavaScript - Size: 107 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 23 - Forks: 2

luffy563/circRNA_tools_comparison

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

Language: Python - Size: 31.9 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 0

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: Python - Size: 86.9 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 1

rdmpage/dimacs-dnabarcode-challenge

Files from DIMACS 2007 DNA barcoding challenge

Language: C - Size: 16.2 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

sean-atkinson/classifying_dna_sequences

A hackathon project attempting to use modelling to correctly identify promoter classes for DNA sequencing.

Language: Jupyter Notebook - Size: 7.2 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

jenetic/covid19-kmer-index

Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification

Language: Python - Size: 307 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

jermp/UST Fork of medvedevgroup/UST

A fork of the original https://github.com/medvedevgroup/UST tool.

Language: C++ - Size: 8.08 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

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: R - Size: 1.73 MB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 0

BiodataAnalysisGroup/kmerGodel

A method for creating a dictionary of all k-mer abundances within a fasta file along with their corresponding Godel numbers.

Language: R - Size: 26.4 MB - Last synced at: 11 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

cmdoret/strangerseq

Generate DNA sequences minimizing microhomology

Language: Go - Size: 48.8 KB - Last synced at: 7 days ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

MislavJaksic/Bioinformatics-Finding-Mutations

Assembles a genome and finds true mutations among sequencing errors

Language: C++ - Size: 76.4 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

mingzhangyang/protein-kmer-signature

An easy way to visualize protein k-mer signature

Language: JavaScript - Size: 30.3 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

johnzhang1999/microbiome

K-mer search enabled fast bacterial DNA sequence retrieval with DNA sequence analysis of Pittsburgh rivers.

Language: Python - Size: 1.85 MB - Last synced at: 7 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

pmenzel/biq

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

Language: JavaScript - Size: 11.8 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0

luislorenzom/hmusket

K-mer spectrum corrector based on Hadoop

Language: Java - Size: 974 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0