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: 16 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

Gulshan-gaur/NAUniSeq

NAUniSeq: A fast computational pipeline to search unique sequences for microbial diagnostics

Language: Python - Size: 853 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - 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: R - Size: 10.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

akcorut/kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Language: Python - Size: 610 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 24 - Forks: 5

jermp/fulgor

Fulgor is a fast and space-efficient colored de Bruijn graph index.

Language: C++ - Size: 13.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 29 - Forks: 7

OndrejSladky/kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

Language: C++ - Size: 5.61 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 11 - Forks: 2

BioJulia/KmerAnalysis.jl

K-mer counting algorithms and count-data utilities for the BioJulia framework

Language: Julia - Size: 5.4 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 12 - Forks: 5

jtnystrom/Discount

Very large scale k-mer counting and analysis on Apache Spark.

Language: Scala - Size: 10.6 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 17 - Forks: 1

kcleal/kmerhash

Convert python string to hashed kmers and back again

Language: Cython - Size: 209 KB - Last synced: 30 days ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

kalyaniasthana/FindingHiddenMessagesInDNA_BioinformaticsI

Coding problems from course 1 of the Bioinformatics specialization

Language: Python - Size: 1.61 MB - Last synced: 6 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

phylo42/RAPPAS

Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

Language: Java - Size: 47.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 9 - Forks: 3

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: 6 months ago - Pushed: 6 months ago - Stars: 12 - Forks: 0

moorembioinfo/KmerAperture

Extract SNPs and accessory differences in closely related bacterial genomes from k-mers

Language: Python - Size: 986 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 0

panthijeeban/Python-Assignment

Python assignment for my Bio-535 course at URI, Spring 2018.

Language: Python - Size: 113 KB - Last synced: 7 months ago - Pushed: about 6 years 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: 8 months ago - Pushed: 8 months ago - Stars: 0 - 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: 1.84 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 7 - 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

shenwei356/kmers

bit-packed k-mers methods for Golang

Language: Go - Size: 17.6 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 8 - Forks: 0

jermp/fulgor-benchmarks

Benchmarks and evaluation scripts for the Fulgor index.

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

bioinfoUQAM/CASTOR_KRFE

Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences

Language: Python - Size: 2.89 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 9 - Forks: 2

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

dib-lab/kmerDecoder

Extract kmers, skipmers, minimizers.

Language: C++ - Size: 584 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 3

victoria-r/BioPython

A collection of various biopython scripts.

Language: Python - Size: 3.76 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

adamjorr/kbbq

reference-free base quality score recalibration

Language: C++ - Size: 2.22 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

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: about 1 year ago - Pushed: about 2 years ago - Stars: 6 - Forks: 0

Selvalakshmi27/Kspectra

Generate K-mer spectra to observe modalities of distributions

Language: Python - Size: 1.49 MB - Last synced: 11 months ago - Pushed: over 1 year 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: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1

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: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

rupeshsure/DNA-Sequence-Classification-Project

DNA CLASSIFICATION

Language: Jupyter Notebook - Size: 6.73 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

phylo42/sherpas

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

Language: C++ - Size: 26.1 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 7 - Forks: 3

polyglotDataNerd/poly-spark-kmers

Language: Scala - Size: 9.71 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

bissim/bgp-d2

This is our implementation for D2 distance algorithm for k-mers.

Language: Java - Size: 2.06 MB - Last synced: about 1 year ago - Pushed: almost 5 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: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0