lh3/yak

Yet another k-mer analyzer

Language: C - Size: 85.9 KB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 108 - Forks: 7

laurentnoe/iedera

subset and spaced seed design tool

Language: C++ - Size: 1.26 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 1

bluenote-1577/sylph

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

Language: Rust - Size: 27.6 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 102 - Forks: 5

liaoherui/VirStrain

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

Language: Python - Size: 6.82 MB - Last synced: about 8 hours ago - Pushed: 2 months ago - Stars: 19 - Forks: 1

deepomicslab/LocalHGT

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

Language: Python - Size: 65.8 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 8 - Forks: 1

steineggerlab/Metabuli

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

Language: C++ - Size: 16.8 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 62 - Forks: 7

bacpop/PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Language: Python - Size: 115 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 79 - Forks: 16

MatthewRalston/kmerdb

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

Language: Python - Size: 23.8 MB - Last synced: about 23 hours ago - Pushed: 2 days ago - Stars: 12 - Forks: 1

bacpop/ska.rust

Split k-mer analysis – version 2

Language: Rust - Size: 532 KB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 54 - Forks: 4

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: 2.76 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 74 - Forks: 16

seqan/raptor

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

Language: C++ - Size: 3.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 47 - Forks: 17

dib-lab/khmer

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

Language: Python - Size: 50.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 729 - Forks: 313

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: 3 months ago - Pushed: 3 months ago - Stars: 76 - Forks: 12

shenwei356/unikmer

a versatile toolkit for k-mers with taxonomic information

Language: Go - Size: 5.72 MB - Last synced: 3 months ago - Pushed: 6 months ago - Stars: 69 - Forks: 7

johnlees/seer

sequence element (kmer) enrichment analysis

Language: C++ - Size: 1.32 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 40 - Forks: 9

seqan/minions

Comparison between different methods to simplify sequence data

Language: C++ - Size: 12.2 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 2

jermp/sshash

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

Language: C++ - Size: 24.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 77 - Forks: 14

CamilaDuitama/decOM

🗑️🦷 decOM 🦷🗑️

Language: Python - Size: 203 MB - Last synced: 8 days ago - Pushed: 6 months ago - Stars: 4 - Forks: 2

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: 3 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

CamilaDuitama/aKmerBroom

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

Language: Python - Size: 6.8 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 1

Chemical118/TRIS

Telomeric Repeat motif Identification tool with Short-read sequencing

Language: C++ - Size: 43.9 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

nf-core/kmermaid 📦

k-mer similarity analysis pipeline

Language: Nextflow - Size: 12.5 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 19 - Forks: 9

mgalardini/pyseer

SEER, reimplemented in python 🐍🔮

Language: Python - Size: 73.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 81 - Forks: 23

ryought/dbgphmm

Probabilistic genome assembler based on de Bruijn Graph and profile HMM

Language: Rust - Size: 2.13 MB - Last synced: 6 months ago - Pushed: 6 months 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: 7 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 1

berybox/KEC

Unique sequence search by K-mer exclusion

Language: Go - Size: 5.53 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 8 - Forks: 0

dib-lab/charcoal

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

Language: Python - Size: 19.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 43 - Forks: 1

suchapalaver/krust

counts k-mers, written in rust

Language: Rust - Size: 23.1 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 26 - Forks: 4

mbhall88/skc

Shared k-mer content between two genomes

Language: Rust - Size: 33.2 KB - Last synced: 5 days ago - Pushed: 11 months 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: 9 months ago - Pushed: about 3 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: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

Language: C++ - Size: 89.8 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 5 - 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: 9 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

aldro61/kover

Learn interpretable computational phenotyping models from k-merized genomic data

Language: Python - Size: 4.38 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 50 - Forks: 16

cmdoret/strangerseq

Generate DNA sequences minimizing microhomology

Language: Go - Size: 48.8 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

mhyfritz/k-mers

Enumerate k-mers of a given string.

Language: JavaScript - Size: 66.4 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

shenwei356/simhash-eval

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

slowikj/seqR

fast and comprehensive k-mer counting package

Language: C++ - Size: 1.72 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 14 - Forks: 1

md5sam/aKmerBroom

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

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

pmenzel/kiq

K-mer indexing and querying in RNA-Seq data

Language: C++ - Size: 77.1 KB - Last synced: about 1 year ago - Pushed: over 5 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: 6 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

RitchieLabIGH/iMOKA

interactive Multi Objective K-mer Analysis

Language: JavaScript - Size: 107 MB - Last synced: 26 days ago - Pushed: about 1 year 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 0

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Language: Perl - Size: 12.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 4 - Forks: 2

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: 10 months ago - Pushed: over 3 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: about 1 year ago - Pushed: over 1 year 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: 11 months ago - Pushed: about 2 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: about 1 year ago - Pushed: about 2 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: about 1 year ago - Pushed: about 2 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: 20 days ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

MislavJaksic/Bioinformatics-Finding-Mutations

Assembles a genome and finds true mutations among sequencing errors

Language: C++ - Size: 76.4 MB - Last synced: about 1 year ago - Pushed: almost 5 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: about 1 year ago - Pushed: over 4 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: about 1 year ago - Pushed: almost 5 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: 7 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

luislorenzom/hmusket

K-mer spectrum corrector based on Hadoop

Language: Java - Size: 974 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0