Kmer概念与工具汇总

Kmer简介

https://en.wikipedia.org/wiki/K-mer](https://en.wikipedia.org/wiki/K-mer
http://www.homolog.us/blogs/2011/09/20/maximizing-utility-of-available-rams-in-k-mer-world/
http://www.homolog.us/blogs/2011/09/20/maximizing-utility-of-available-rams-in-k-mer-world/
http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html](http://koke.asrc.kanazawa-u.ac.jp/HOWTO/kmer-genomesize.html)

Kmer分析工具汇总

Jellyfish：https://github.com/gmarcais/Jellyfish/releases/

kmer-conut：https://github.com/alexpreynolds/kmer-counter。

K-mer Analysis Toolkit (KAT)：https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408915/
https://github.com/TGAC/KAT

R包kmer：https://rdrr.io/rforge/Kmer/
https://cran.r-project.org/web/packages/kmer/vignettes/kmer-vignette.html

R包kmeRs：https://rdrr.io/cran/kmeRs/

python包khmer：https://khmer.readthedocs.io/en/v2.1.1/

python包stringMLST：Fast k-mer based tool for multi locus sequence typing (MLST) https://github.com/jordanlab/stringMLST

kmer统计脚本：https://noble.gs.washington.edu/proj/nucsvm/fasta2matrix.py

参考链接

Question: Counting k-mers in a multifasta file https://www.biostars.org/p/247336/
https://noble.gs.washington.edu/proj/nucsvm/
https://www.biostars.org/p/286438/
K-Mer Analysis：https://www.biostars.org/p/50207/
https://www.ebi.ac.uk/about/events/seminars/2018/k-mer-methods-sequencing-data-analysis