14 results found Sort:

dib-lab
khmer dib-lab
295
749
other
68
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dna k-mer python bloom-filter bioinformatics graph-traversal count-min-sketch
Created 2012-05-15
6,672 commits to master branch, last one 5 years ago
bluenote-1577
sylph bluenote-1577
6
136
mit
3
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
k-mer metagenomics sketching-algorithm taxonomic-classification average-nucleotide-identity
Created 2023-05-06
248 commits to main branch, last one 21 days ago
lh3
yak lh3
8
113
mit
8
Yet another k-mer analyzer
k-mer bioinformatics
Created 2019-10-11
71 commits to master branch, last one 5 months ago
mgalardini
pyseer mgalardini
27
109
apache-2.0
10
SEER, reimplemented in python 🐍🔮
gwas k-mer bacteria reimplementation reproducible-science
Created 2017-09-22
541 commits to master branch, last one 24 days ago
steineggerlab
Metabuli steineggerlab
9
108
gpl-3.0
5
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
k-mer taxonomy metagenomics bioinformatics taxonomic-classification
Created 2020-09-09
3,042 commits to master branch, last one 6 days ago
bacpop
PopPUNK bacpop
18
89
apache-2.0
6
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
k-mer bacteria genomics sketching population-genetics
Created 2018-01-09
2,230 commits to master branch, last one 8 days ago
pirovc
ganon pirovc
13
87
mit
4
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 hierar...
gtdb ncbi k-mer refseq genbank taxonomy microbiome minimizers bloom-filter metagenomics bioinformatics
Created 2018-08-30
690 commits to master branch, last one 7 months ago
refresh-bio
kmer-db refresh-bio
16
83
gpl-3.0
7
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
k-mer genomics indexing bioinformatics sequence-similarity
Created 2018-02-09
181 commits to master branch, last one 15 days ago
jermp
sshash jermp
17
83
mit
5
A compressed, associative, exact, and weighted dictionary for k-mers.
k-mer hashing dictionary bioinformatics minimal-perfect-hash
Created 2022-01-13
225 commits to master branch, last one a day ago
shenwei356
unikmer shenwei356
7
75
mit
3
A versatile toolkit for k-mers with taxonomic information
set kmer unik k-mer union golang unique difference intersection
Created 2018-08-09
423 commits to master branch, last one about a month ago
bacpop
ska.rust bacpop
4
57
apache-2.0
4
Split k-mer analysis – version 2
ska rust k-mer sequence alignment bioinformatics
Created 2022-11-08
319 commits to master branch, last one 2 days ago
dib-lab
charcoal dib-lab
1
52
other
19
Remove contaminated contigs from genomes using k-mers and taxonomies.
k-mer sourmash metagenomics bioinformatics
Created 2020-03-09
336 commits to latest branch, last one 2 years ago
seqan
raptor seqan
18
52
other
4
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
k-mer filter binning minimizer threshold bloom-filter set-membership
Created 2020-09-11
880 commits to main branch, last one 2 days ago
aldro61
kover aldro61
14
50
gpl-3.0
7
Learn interpretable computational phenotyping models from k-merized genomic data
k-mer genomics phenotypes machine-learning biomarker-discovery
Created 2015-06-01
314 commits to kover2 branch, last one 2 years ago