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kmer

Here are 59 public repositories matching this topic...

jerryji1993 / DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

nlp machine-learning natural-language-processing deep-learning genome gpu sequence kmer dnabert-model kmer-format

Updated Aug 27, 2021
Python

smudgeplot

KamilSJaron / smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

bioinformatics genomics kmer

Updated Feb 21, 2022
R

mcveanlab / mccortex

De novo genome assembly and multisample variant calling

genomics variant-calling kmer cortex genome-analysis genome-assembly de-bruijn-graphs genome-graph contigs

Updated Mar 28, 2019
C

kmcp

shenwei356 / kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

sketch metagenomics sketching cobs kmer searching virome taxonomic-classification taxonomic-profiling scaled-minhash syncmers bigsi fracminhash

Updated Mar 18, 2022
Go

shenwei356 / unikmer

Toolkit for nucleic acid k-mer analysis, including set operations on k-mers (sketch) optional with TaxIDs but without count information.

golang set union intersection kmer k-mer difference unique unik

Updated Mar 3, 2022
Go

edawson / rkmh

Classify sequencing reads using MinHash.

bioinformatics nanopore openmp mutations minhash kmer

Updated Apr 6, 2020
C++

jordanlab / stringMLST

Fast k-mer based tool for multi locus sequence typing (MLST)

python bioinformatics mlst kmer bacterial-database fastq-files bacterial-genomes applied-bioinformatics-lab

Updated Sep 3, 2020
Python

OpenGene / UniqueKMER

Generate unique KMERs for every contig in a FASTA file

bioinformatics virus ngs sequencing fasta kmer unique

Updated Jul 28, 2020
C

andrewjpage / tiptoft

Predict plasmids from uncorrected long read data

bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

Updated Dec 5, 2019
Python

tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections

count bloom-filters matrix kmer

Updated Mar 11, 2022
C++

edawson / mkmh

Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.

minhash locality-sensitive-hashing kmer

Updated Jan 9, 2021
C++

IQTLabs / freqgen

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies

genetic-algorithm fasta kmer codon-usage

Updated Jan 13, 2022
Python

alexpreynolds / kmer-counter

Count kmers with a more efficient (faster) hash table

bioinformatics genomics cpp14 hash-map kmer kmer-counting

Updated Sep 12, 2020
C++

brentp / nim-kmer

Sponsor

DNA kmer operations for nim

genomics kmer nim-lang

Updated May 27, 2021
Nim

STing

jordanlab / STing

Ultrafast sequence typing and gene detection from NGS raw reads

ubuntu genomics cpp zlib ngs computational-biology databases dna genes mlst kmer autotools locus ngs-analysis cgmlst sting-applications

Updated Apr 15, 2021
C++

nf-core / kmermaid

k-mer similarity analysis pipeline

workflow pipeline nextflow kmer k-mer kmer-frequency-count kmer-counting nf-core

Updated Mar 17, 2022
Nextflow

slowikj / seqR

fast and comprehensive k-mer counting package

Updated Sep 27, 2021
C++

zhangrengang / SubPhaser

Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers.

kmer phase allopolyploid subgenome

Updated Mar 15, 2022
Python

BioJulia / KmerAnalysis.jl

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

kmer kmer-frequency-count kmer-distribution kmer-counting biojulia kmer-composition kmers kmer-spectra

Updated Aug 29, 2020
Julia

suchapalaver / krust

k-mer counter in Rust using the rust-bio and rayon crates

rust kmer k-mer k-mer-counting rayon kmer-counting kmers k-mers rust-bio dashmap

Updated Jan 29, 2022
Rust

AlgoLab / rs-vgaligner

Rust implementation of ekg's dozyg

rust bioinformatics anchors alignment kmer poa chaining

Updated Mar 17, 2022
Rust

metageni / FOCUS

FOCUS: An Agile Profiler for Metagenomic Data

bioinformatics microbiome kmer metagenomes identify-organisms

Updated Dec 31, 2021
Python

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.

kmer fasta-sequences kmer-frequency-count kmer-counting fasta-format kmers kmer-length

Updated Jun 30, 2021
Python

wrf / lavaLampPlot

instructions, python and R code for generating lava lamp plots of kmer coverage

visualization quality-control genomics metagenomics rshiny kmer lavalampplot

Updated Jan 16, 2022
Python

lzhLab / kmcEx

ngs kmer encoding-kmers

Updated Nov 29, 2019
C++

alexpreynolds / kmer-collapse

Collapse a set of redundant kmers to use IUPAC degenerate bases

encoding bioinformatics kmer iupac

Updated Nov 26, 2021
Python

mooreryan / eigengenomes

A C and Python implementation of latent strain analysis for eigengenome partitioning.

bioinformatics clustering assembly metagenomics partitioning kmer hyperplane

Updated Mar 11, 2017
C

shenwei356 / unik

A k-mer serialization package for Golang

serialization taxid kmer kmer-file

Updated Nov 8, 2021
Go

jlanga / exfi

Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools

rna-seq network assembly bloom-filter conda pandas python3 biopython bioconda kmer transcriptome transcriptomics bedtools exon abyss splice-graphs biobloomtools abyss-bloom

Updated Jul 28, 2020
Python

RobinPetit / SeedTrick

Implementation of some (multiple) instance kernels

spectrum svm kmer kittens kernel-functions suffix-tree odh comik

Updated May 30, 2019
Python

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