k-mer 开源项目推荐（91 个）

dib-lab /khmer

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

bluenote-1577 /sylph

通过丰度校正的 minhash 对宏基因组样本进行超快分类学分析和基因组查询。

steineggerlab /Metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

lh3 /yak

Yet another k-mer analyzer

mgalardini /pyseer

SEER, reimplemented in python 🐍🔮

bacpop /PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

bacpop /ska.rust

Split k-mer analysis – version 2

pirovc /ganon

ganon2 能高效地将基因组序列与大型参考集进行分类，集成了数据库下载和更新（refseq/genbank）、分类学分析（ncbi/gtdb）、分箱和层次分类、自定义报告等功能

jermp /sshash

📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.

refresh-bio /kmer-db

Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour.

shenwei356 /unikmer

A versatile toolkit for k-mers with taxonomic information

Sh1ne111 /KMERIA

A KMER-based genome-wIde Assocation testing approach on polyploids

dib-lab /charcoal

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

seqan /raptor

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

aldro61 /kover

Learn interpretable computational phenotyping models from k-merized genomic data

johnlees /seer

sequence element (kmer) enrichment analysis

Plant-Food-Research-Open /assemblyqc

A Nextflow pipeline for evaluating assembly quality

bacpop /sketchlib.rust

Fast sequence distance estimates

suchapalaver /kmerust

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

RitchieLabIGH /iMOKA

interactive Multi Objective K-mer Analysis