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The Top 23 Bioinformatics Kmer Open Source Projects

Open source projects categorized as Bioinformatics Kmer
Categories > Data Processing > Bioinformatics
Categories > Kmer
Khmer ⭐ 729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dependent packages 7total releases 18most recent commit 2 years agopypi khmer} Downloads
Sourmash ⭐ 431
Quickly search, compare, and analyze genomic and metagenomic data sets.
dependent packages 16total releases 67most recent commit 7 days agopypi sourmash} Downloads
Smudgeplot ⭐ 200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
most recent commit 3 months ago
Spacegraphcats ⭐ 112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
total releases 15most recent commit 3 months ago
Mccortex ⭐ 86
De novo genome assembly and multisample variant calling
most recent commit 5 years ago
Yak ⭐ 83
Yet another k-mer analyzer
most recent commit a year ago
Sshash ⭐ 77
A compressed, associative, exact, and weighted dictionary for k-mers.
most recent commit 3 months ago
Ganon ⭐ 73
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
most recent commit 3 months ago
Kmer Db ⭐ 68
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
most recent commit a year ago
Metabuli ⭐ 54
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
most recent commit 3 months ago
Ska.rust ⭐ 35
Split k-mer analysis – version 2
total releases 14most recent commit 5 months ago
Uniquekmer ⭐ 33
Generate unique KMERs for every contig in a FASTA file
most recent commit 2 years ago
Lphash ⭐ 33
Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
most recent commit 9 months ago
Rkmh ⭐ 32
Classify sequencing reads using MinHash.
most recent commit 4 years ago
Charcoal ⭐ 31
Remove contaminated contigs from genomes using k-mers and taxonomies.
most recent commit 2 years ago
Prophyle ⭐ 30
Accurate, resource-frugal and deterministic DNA sequence classifier.
total releases 53most recent commit 4 months ago
Stringmlst ⭐ 27
Fast k-mer based tool for multi locus sequence typing (MLST)
total releases 20most recent commit 4 years ago
Krust ⭐ 26
counts k-mers, written in rust
most recent commit 7 months ago
Phist ⭐ 22
Phage-Host Interaction Search Tool
most recent commit 7 months ago
Fulgor ⭐ 22
A fast and compact k-mer index for large-scale matching and color queries.
most recent commit 3 months ago
Tiptoft ⭐ 20
Predict plasmids from uncorrected long read data
total releases 6most recent commit 4 years ago
Kgwasflow ⭐ 19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
most recent commit 6 months ago
Mof Search ⭐ 18
BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours
most recent commit 4 months ago
The 2 Most Depended On Bioinformatics Kmer Open Source Projects
Sourmash ⭐ 431
Quickly search, compare, and analyze genomic and metagenomic data sets.
dependent packages 16total releases 67latest release September 15, 2023most recent commit 7 days agopypi sourmash} Downloads
Khmer ⭐ 729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dependent packages 7total releases 18latest release December 15, 2021most recent commit 2 years agopypi khmer} Downloads
The 10 Latest Releases In Bioinformatics Kmer Open Source Projects
Ska.rust ⭐ 35
Split k-mer analysis – version 2
total releases 14latest release November 23, 2023most recent commit 5 months ago
Sourmash ⭐ 431
Quickly search, compare, and analyze genomic and metagenomic data sets.
dependent packages 16total releases 67latest release September 15, 2023most recent commit 7 days agopypi sourmash} Downloads
Skc ⭐ 12
Shared k-mer content between two genomes
total releases 1latest release June 20, 2023most recent commit 10 months ago
Discount ⭐ 14
Very large scale k-mer counting and analysis on Apache Spark.
total releases 6latest release February 13, 2023most recent commit a year ago
Spacegraphcats ⭐ 112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
total releases 15latest release December 04, 2022most recent commit 3 months ago
Focus ⭐ 5
FOCUS: An Agile Profiler for Metagenomic Data
total releases 5latest release December 28, 2021most recent commit 2 years ago
Khmer ⭐ 729
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dependent packages 7total releases 18latest release December 15, 2021most recent commit 2 years agopypi khmer} Downloads
Seqr ⭐ 8
fast and comprehensive k-mer counting package
total releases 1latest release September 15, 2021most recent commit 3 years ago
Prophyle ⭐ 30
Accurate, resource-frugal and deterministic DNA sequence classifier.
total releases 53latest release August 23, 2021most recent commit 4 months ago
Stringmlst ⭐ 27
Fast k-mer based tool for multi locus sequence typing (MLST)
total releases 20latest release September 02, 2020most recent commit 4 years ago
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