k-mers
There are 34 repositories under k-mers topic.
spacegraphcats/spacegraphcats
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
bioinformatics-centre/BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
bingmann/cobs
COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
imartayan/CBL
A Rust library providing fully dynamic sets of k-mers with high locality
jermp/lphash
Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
liaoherui/StrainScan
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
prophyle/prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
suchapalaver/krust
Bioinformatics 101 tool for counting unique k-length substrings in DNA
refresh-bio/PHIST
Phage-Host Interaction Search Tool
prophyle/prophasm
ProphAsm β a rapid computation of simplitigs directly from k-mer sets
karel-brinda/Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
algbio/SBWT
Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
karel-brinda/MiniPhy
Phylogenetic compression of extremely large genome collections [661k βππ²ππΆπ | BIGSIdata βπ°π΄ππΆπ | AllTheBact'23 βπ³π±ππΆπ]
hannesbecher/shiny-k-mers
Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
OndrejSladky/kmercamel
KmerCamelπ« provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
microbial-pangenomes-lab/panfeed
A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.
hoseinlook/bioinformatic-course
simple virus DNA classification
ITBE-Lab/seed-evaluation
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
prophyle/prophex
ProPhex β an exact k-mer index using Burrows-Wheeler Transform
hannesbecher/genome-size-variation
Investigating genome size variation with k-mers
karel-brinda/de-MiniPhy-BIGSIdata
Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs
sirineFoudili/DNA-comparison-and-alignment-
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
visheshsinha/DNA-Sequencing
Get Started with DNA Sequencing working with .FastQ and .FastA file formats and performing Pattern Matching Algorithms (Exact & Approximate).
enricorox/USTAR2
A compressor for k-mers sets with counters
eskutkaan-zz/biodata
a molecular solutions toolbox for molecular biologists.
peteashton/mininorm
Minimiser-based digital normalisation for long-read DNA sequence datasets
hannesbecher/excess-variance
Excess variance in k-mer spectra
jenetic/covid19-kmer-index
Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification
leonardoGemin/Bioinformatics_UniPd
Project for the course of Bioinformatics - University of Padua.
maremita/phd_projects
Thesis projects
oliadikan/thesis_source
Source files created during the Master's Thesis
BiodataAnalysisGroup/kmerAnalyzer
An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.
DamienLegros/kmers
Projet GENOM master 2 BIM : 2022 - 2023 Projet de bio-informatique sur les k-mers codΓ© en Python
karel-brinda/phylogenetic-compression-supplement
Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"