Topic: "kmers"
jermp/fulgor
⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.
Language: C++ - Size: 14 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 50 - Forks: 11
suchapalaver/krust
Bioinformatics 101 tool for counting unique k-length substrings in DNA
Language: Rust - Size: 23.1 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 30 - Forks: 5
akcorut/kGWASflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Language: Python - Size: 610 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 5
jtnystrom/Discount
Very large scale k-mer counting and analysis on Apache Spark.
Language: Scala - Size: 10.6 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 18 - Forks: 2
slowikj/seqR
fast and comprehensive k-mer counting package
Language: C++ - Size: 1.72 MB - Last synced at: 21 days ago - Pushed at: over 3 years ago - Stars: 18 - Forks: 1
OndrejSladky/kmercamel
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
Language: C++ - Size: 8.06 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 2
arminZolfaghari/DNA-Sequence-Classification
Analysis of DNA Sequence Classification Using Neural Networks - Bioinformatics Course Project - Winter 2022
Language: Jupyter Notebook - Size: 8.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 0
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)
Language: R - Size: 1.69 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 11 - Forks: 1
BioJulia/KmerAnalysis.jl
K-mer counting algorithms and count-data utilities for the BioJulia framework
Language: Julia - Size: 5.4 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 5
phylo42/RAPPAS
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Language: Java - Size: 47.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 3
bioinfoUQAM/CASTOR_KRFE
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
Language: Python - Size: 2.89 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 2
dib-lab/kmerDecoder
Extract kmers, skipmers, minimizers.
Language: C++ - Size: 584 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 3
suchapalaver/fastas2kmers
A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.
Language: Python - Size: 17.6 KB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 0
shenwei356/kmers
bit-packed k-mers methods for Golang
Language: Go - Size: 17.6 KB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0
phylo42/sherpas
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences
Language: C++ - Size: 26.1 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 3
moorembioinfo/KmerAperture
Extract SNPs and accessory differences in closely related bacterial genomes from k-mers
Language: Python - Size: 986 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
kcleal/kmerhash
Convert python string to hashed kmers and back again
Language: Cython - Size: 209 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
GioStamoulos/Kmers_Dataset_Generation_Regression_Clustering
The generation of a kmers dataset that is associated with multiple gene sequences and the further manipulation of this generated dataset are the main contents of the current project.
Language: Jupyter Notebook - Size: 50.1 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0
adamjorr/kbbq
reference-free base quality score recalibration
Language: C++ - Size: 2.22 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
Gulshan-gaur/NAUniSeq
NAUniSeq: A fast computational pipeline to search unique sequences for microbial diagnostics
Language: Python - Size: 979 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0
Selvalakshmi27/Kspectra
Generate K-mer spectra to observe modalities of distributions
Language: Python - Size: 1.49 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
polyglotDataNerd/poly-spark-kmers
Language: Scala - Size: 9.71 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0
maremita/slm_kgenomvir
Evaluation of Statistical Linear Models for Genome Virus Classification
Language: Jupyter Notebook - Size: 3.12 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 1
bitlab-tech/sequence_analysis_security-study
Security & performance assessment on client-server schemes that perform genomic sequence analysis using different encryption methods
Language: Rust - Size: 258 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
Louis-MG/META-DIFF
This is the repository of the pipeline META-DIFF, which detects sequences in differential abundances between two conditions, and annotates them taxonomicaly and functionaly.
Language: Python - Size: 12.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
IBCHgenomic/sequenceprofiler
rust graph and sequence profiler for reads and genomes
Language: Rust - Size: 6.49 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
urniaz/HeatMap4kmeRs
Visualization package for kmeRs similarity score matrix
Language: Python - Size: 398 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
gabrielecanesi/DNA-SNP-finder
An algorithm for finding SNPs of a long read compared to a reference genome
Language: C++ - Size: 148 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
jermp/fulgor-benchmarks
Benchmarks and evaluation scripts for the Fulgor index.
Size: 0 Bytes - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
victoria-r/BioPython
A collection of various biopython scripts.
Language: Python - Size: 3.76 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
rupeshsure/DNA-Sequence-Classification-Project
DNA CLASSIFICATION
Language: Jupyter Notebook - Size: 6.73 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
maremita/CASTOR_KRFE_v1.0
[Features extraction method] You can find the new version of CASTOR_KRFE at https://github.com/bioinfoUQAM/CASTOR_KRFE
Language: Python - Size: 1.94 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0
bissim/bgp-d2
This is our implementation for D2 distance algorithm for k-mers.
Language: Java - Size: 2.06 MB - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
andriusbern/afp
Alignment-Free phylogenetic tree construction from .fasta sequence files
Language: C++ - Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
kalyaniasthana/FindingHiddenMessagesInDNA_BioinformaticsI
Coding problems from course 1 of the Bioinformatics specialization
Language: Python - Size: 1.61 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
panthijeeban/Python-Assignment
Python assignment for my Bio-535 course at URI, Spring 2018.
Language: Python - Size: 113 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
