基因组K-mer分析（二代）-step1

GitHub - TGAC/KAT: The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

在基因组组装之前需要做！

进入conda环境

conda activate kat

K-mer comparison tool.

Creates a matrix of shared K-mers between two (or three) sequence files or hashes.

kat comp -t 10 -n -o katcomp /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_1.fq.clean /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_2.fq.clean

plot: Plotting tools.

Contains several plotting tools to visualise K-mer and compare distributions.

kat plot spectra-mx -i -x 200 -o kat_spectra.png katcomp-main.mx

K-mer GC Processor.

Creates a matrix of the number of K-mers found given a GC count and a K-mer count.

kat gcp -t 10 -m 27 /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_1.fq.clean /media/aa/DATA/SZQ2/bj/my/genome/5.1210/01cleandata/A5.1210.L350_FDSW22H000294-3r_2.fq.clean