pfeiferd/genestrip-db

A selection of databases for Genestrip

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pfeiferd/genestrip

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

Language: Java - Size: 94.6 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 6 - Forks: 0

quinlan-lab/constraint-tools

Tools to discover natural selection given multiple evolved DNA sequences (e.g., gnomad cohort, or multiple tumor samples)

Language: Jupyter Notebook - Size: 601 MB - Last synced at: 23 days ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

tseemann/kounta

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

Language: Perl - Size: 93.8 KB - Last synced at: 12 days ago - Pushed at: about 5 years ago - Stars: 12 - Forks: 3

gi-bielefeld/pangrowth

Pangenome openness from k-mers or genes

Language: C - Size: 19.5 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 4 - Forks: 0

nf-core/kmermaid

k-mer similarity analysis pipeline

Language: Nextflow - Size: 12.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 20 - Forks: 13

Qile0317/KmerGMA.jl

A seed-based homology searching tool

Language: Julia - Size: 1.55 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

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

BioJulia/KmerAnalysis.jl

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

Language: Julia - Size: 5.4 MB - Last synced at: 8 days ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 5

jtnystrom/Discount

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

Language: Scala - Size: 10.6 MB - Last synced at: 36 minutes ago - Pushed at: about 1 year ago - Stars: 18 - Forks: 2

alexpreynolds/kmer-counter

Count kmers with a more efficient (faster) hash table

Language: C++ - Size: 44.9 KB - Last synced at: 13 days ago - Pushed at: 11 months ago - Stars: 24 - Forks: 5

suchapalaver/krust

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

Language: Rust - Size: 23.1 MB - Last synced at: 20 days ago - Pushed at: over 1 year ago - Stars: 30 - Forks: 5

PASSIONLab/ELBA

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

Language: C++ - Size: 106 MB - Last synced at: 9 months ago - Pushed at: 11 months ago - Stars: 14 - Forks: 9

crosenth/moose

dna/rna alignment classifier

Language: Python - Size: 1.08 MB - Last synced at: 12 days ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

angelovangel/fastkmers

Obtain k-mer counts from fastx files

Language: Rust - Size: 72.3 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - 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 at: 14 days ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 0

lvn3668/KmerCounter

Kmer counter is written in GO Lang v 1.16.5 To install GO on Windows, follow the instructions at https://golang.org/doc/install 4 GO implementation of N-mer counter in DNA sequences which tests for validity of input. It reads in file name (of fasta file) It reads the size length (kmer length) for which counts are desired and writes out to file, counts of all overlapping kmers of size 1 through the specified input. It checks if fasta file is empty amd whether kmer length is specified.

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petermchale/genomics-web-app

vue app with flask REST api to process genomic data

Language: Jupyter Notebook - Size: 49.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

TayHuiYi/kmer-counting

Bioinformatics

Size: 184 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

alexpreynolds/kmer-counter-abseil

Count canonical kmers with Abseil C++ `absl::flat_hash_map`

Language: C++ - Size: 8.79 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

rejoyc-cs/k_mer_in_DNA

Counts the number of occurrences of each k-mer in a DNA string

Language: Python - Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

victoria-r/PythonProjects

Various python projects.

Language: Python - Size: 249 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

jacobjmarks/SPK-counter 📦

Fast and memory-efficient "single pass" kmer counting

Language: C++ - Size: 35.2 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

GZHoffie/kmer-count

Implementation of k-mer counting algorithms BFCounter and experimental implementation of Misra-Gries. The goal is to use as little memory as possible.

Language: Java - Size: 18.6 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Anonymous7code/Machine-Learning

This is the Machine learning Project Repo.

Language: Jupyter Notebook - Size: 1.32 GB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

jdisset/kmap

Represents sequences files in fasta format in terms of their kmer counts.

Language: C++ - Size: 2.7 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

at-cg/MMC

Minimizer counting and analysis

Language: C++ - Size: 4.56 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

mjoppich/tsxCount

Language: C++ - Size: 1.34 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Kingsford-Group/hierrepsetselection

Select representative sequencing data sets.

Language: Python - Size: 50.8 KB - Last synced at: 7 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

arriam-lab2/yack

fast and lightweight counting of short k-mers

Language: Python - Size: 170 KB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Lizhen0909/SpaRC-MPI

MPI version of Sparc

Language: C++ - Size: 1.7 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 2

alexpreynolds/kmer-counter-boost

Count canonical kmers with Boost C++ `boost::unordered_map` hash table

Language: C++ - Size: 7.81 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

alexpreynolds/kmer-counter-emilib

Count canonical kmers with Emil Ernerfeldt's emilib::HashMap

Language: C++ - Size: 10.7 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

alexpreynolds/kmer-counter-ska

Count canonical kmers with Malte Skarupke's bytell_hash_map hash table

Language: C++ - Size: 23.4 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

alexpreynolds/kmer-counter-sparse

Count canonical kmers with Google sparse_hash_map

Language: C++ - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

alexpreynolds/kmer-counter-unordmap

Count canonical kmers with STL unordered_map

Language: C++ - Size: 15.6 KB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0