#

k-mer

Here are 38 public repositories matching this topic...

dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

python bioinformatics bloom-filter dna count-min-sketch k-mer graph-traversal

Updated Mar 31, 2021
Python

lh3 / yak

Yet another k-mer analyzer

bioinformatics k-mer

Updated Dec 25, 2021
C

mgalardini / pyseer

SEER, reimplemented in python 🐍

🔮

gwas reproducible-science reimplementation bacteria k-mer

Updated Jul 19, 2021
Python

pirovc / ganon

a read classification tool based on Interleaved Bloom Filters

bioinformatics bloom-filter metagenomics k-mer

Updated Feb 3, 2022
Python

aldro61 / kover

Learn interpretable computational phenotyping models from k-merized genomic data

machine-learning genomics k-mer phenotypes biomarker-discovery

Updated Aug 10, 2021
Python

johnlees / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

genomics sketching bacteria k-mer population-genetics

Updated Jan 21, 2022
Python

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 Nov 22, 2021
Go

jermp / sshash

A compressed, associative, exact dictionary for k-mers.

hashing bioinformatics k-mer minimal-perfect-hash

Updated Feb 4, 2022
C++

johnlees / seer

sequence element (kmer) enrichment analysis

gwas bacteria k-mer

Updated Mar 4, 2021
C++

seqan / raptor

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

filter bloom-filter threshold binning k-mer minimizer set-membership

Updated Feb 9, 2022
C++

prophyle / prophyle

Accurate, resource-frugal and deterministic DNA sequence classifier.

bioinformatics metagenomics viruses bwt bacteria k-mer phylogeny metagenomic-classification taxonomic-classification

Updated Feb 1, 2022
Python

dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

bioinformatics metagenomics k-mer sourmash

Updated Jan 29, 2022
Python

iMOKA

RitchieLabIGH / iMOKA

interactive Multi Objective K-mer Analysis

machine-learning gui angular singularity data-analysis k-mer rna-seq-analysis

Updated Dec 17, 2021
JavaScript

nf-core / kmermaid

k-mer similarity analysis pipeline

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

Updated Dec 14, 2021
Nextflow

slowikj / seqR

fast and comprehensive k-mer counting package

Updated Sep 27, 2021
C++

liaoherui / VirStrain

An RNA virus strain-level identification tool for short reads.

virus metagenomics k-mer reference-database strain

Updated Feb 9, 2022
HTML

MatthewRalston / kmerdb

Open

fileutil.py habitually raises StopIteration errors. Needs triage.

MatthewRalston commented Jan 22, 2022

Traceback (most recent call last):
  File "/home/matt/.pyenv/versions/kdb/bin/kmerdb", line 33, in <module>
    sys.exit(load_entry_point('kmerdb==0.5.2', 'console_scripts', 'kmerdb')())
  File "/home/matt/.pyenv/versions/kdb/lib/python3.10/site-packages/kmerdb-0.5.2-py3.10.egg/kmerdb/__init__.py", line 1639, in cli
    args.func(args)
  File "/home/matt/.pyenv/versions/kdb/lib/pytho

Read more

bug documentation help wanted good first issue

Open

Urgent help needed in matrix pass

Open

Larger look into the uint64 space, choosing the best k for my machine

6

Find more good first issues

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

pmenzel / kiq

K-mer indexing and querying in RNA-Seq data

rna-seq k-mer transcriptomics k-mer-counting

Updated Jan 23, 2019
C++

tobiasrausch / rdxon

Reference-free FASTQ filter for rare germline and somatic variants

sequencing cancer-genomics variant-calling k-mer pan-genome rare-disease reference-free

Updated Jul 14, 2021
C++

bioinfo-ut / AluMine

Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes

genomics k-mer alu repeatmasker transposable-element alignment-free-algorithm

Updated Feb 3, 2021
Perl

BioGenies / CancerGram

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI.

bioinformatics r-package k-mer peptide-identification random-forests n-gram anticancer-peptides

Updated Nov 19, 2020
R

akiomiyao / ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

inversion ngs insertion snp polymorphism k-mer sequence-alignments variant somatic-mutations genotype deletion ngstools alignment-free-algorithm

Updated Jan 21, 2022
Perl

zmmason / BINF

Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

markov-chain motif dna fasta mass-spectrometry k-mer genome-analysis peptides de-bruijn-graphs fasta-sequences orf protein-sequence z-score directed-acyclic-graph overlap-graph cyclic-peptides cyclic-pattern

Updated Jan 28, 2021
Python

laurentnoe / iedera

subset and spaced seed design tool

indexing k-mer sequence-alignments alignment-free sequence-alignment read-mapping metagenomic-classification align spaced-seed

Updated Feb 2, 2022
C++

pmenzel / biq

Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets

rna-seq k-mer transcriptomics circrna sra circular-rna backsplice-junction

Updated Mar 14, 2019
JavaScript

shenwei356 / go-hashing-kmer-bench

Benchmark of hashing k-mers in Golang

hashing xxhash kmer k-mer wyhash nthash

Updated Jan 17, 2021
Go

Scien-ide / Helix

A PHP hash table optimized for counting short gene sequences for use in Bioinformatics.

php bioinformatics bloom-filter dna fasta k-mer fastq k-mer-counting dna-sequences 2bit canonical

Updated Jun 22, 2021
PHP

BiodataAnalysisGroup / kmerGodel

A method for creating a dictionary of all k-mer abundances within a fasta file along with their corresponding Godel numbers.

k-mer godel-numbering

Updated Jan 5, 2021
R

benvenutti / ganon

A read classification tool based on Interleaved Bloom Filters

bioinformatics cmake bloom-filter metagenomics cpp17 k-mer

Updated Feb 20, 2021
Python

Improve this page

Add a description, image, and links to the k-mer topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with the k-mer topic, visit your repo's landing page and select "manage topics."