Jellyfish + GenomeScope估计基因组大小及杂合度

genomescope2.0

一、安装

conda create -n jellyfish jellyfish

二、使用

conda activate jellyfish
bash jellyfish.sh

#脚本文件如下

#!/bin/bash
#program:
#run jellyfish to genetate .histo file

cd ~/00bam2fastq
gunzip *.fastq.gz
jellyfish count -C -m 21 -s 1000000000 -t 16 *.fastq -o reads.jellyfish
jellyfish histo -t 16 reads.jellyfish > reads.histo

三、作图

reads.histo上传到genomescope网站，默认参数作图即可。这个网站后台内存经常被占满导致文件上传失败（no file uploaded），过一段时间再提交即可。