「基因组」判断物种倍性

鉴定基因组倍性判断方法：

1.smudgeplot
2.PloidyFrost
3.Survey软件：genomescope2(根据survey峰图判断)
4.与近缘二倍体做比较，基因组大小，基因组共线性，基因共线性，如果是植物，比如有胚植物，可结合busco D值观察，结合核型和HiC图。

1.smudgeplot

下载地址：https://github.com/KamilSJaron/smudgeplot
conda装，超级多依赖。
注意：目前已经到v0.4.0版本，与0.1.2.5低版本存在较大改变，kmer 计数软件改变，消耗内存较大，基因组较大时比较慢，可能大基因组会中断。

2.ploidyfrost

下载地址：https://github.com/CMB-BNU/PloidyFrost
ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs

NGS数据分析：

mkdir kmc_tmp 
export PATH=/share/nas1/pengzw/software/PloidyFrost/KMC/bin/:$PATH
export PATH=/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bin/:$PATH
export PATH=/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bifrost/bin/:$PATH

thread=20
fq=fq.list
#/share/nas1/pengzw/project/01.data/Unknown_good_1.fq
#/share/nas1/pengzw/project/01.data/Unknown_good_2.fq
out_fq=out_fq.list
kmc -ci1 -cs10000 -k25 -t${thread} @${fq} kmc_db kmc_tmp
kmc_tools transform kmc_db histogram hist
lower_threshold=$(PloidyFrost cutoffL hist)
kmc_tools -t${thread} filter -hm kmc_db @${fq} -ci${lower_threshold} sample_filtered.fq


Bifrost build -i -d -k 25 -v -r sample_filtered.fq -o dbg -t ${thread}

PloidyFrost -g dbg.gfa -d kmc_db -t ${thread} -v -o multi -h hist
cd PloidyFrost_output
Rscript  /share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/script/Filter.R -i multi -o multi-filtered -n 6 -s 11 -q 0.05
Rscript /share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/script/Drawfreq.R -f multi-filtered_allele_frequency.txt -t title -p 2 -o histogram
/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bin/PloidyFrost model -g multi-filtered_allele_frequency.txt -l 1 -u 10 -q 0.05 -o gmm

2.TGS数据分析

mkdir kmc_tmp 
export PATH=/share/nas1/pengzw/software/PloidyFrost/KMC/bin/:$PATH
export PATH=/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bin/:$PATH
export PATH=/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bifrost/bin/:$PATH

thread=20
fq=/share/nas1/pengzw/project/01.rawdata/ccs/.ccs.fasta.gz
kmc -ci1 -cs10000 -k25 -t${thread}  -fa $fq  kmc_db kmc_tmp
kmc_tools transform kmc_db histogram hist
lower_threshold=$(PloidyFrost cutoffL hist)
kmc_tools -t${thread} filter -hm kmc_db $fq -ci${lower_threshold} sample_filtered.fq


Bifrost build -i -d -k 25 -v -r sample_filtered.fq -o dbg -t ${thread}

PloidyFrost -g dbg.gfa -d kmc_db -t ${thread} -v -o single -h hist
cd PloidyFrost_output
Rscript  /share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/script/Filter.R -i single -o single-filtered -n 6 -s 11 -q 0.05
Rscript /share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/script/Drawfreq.R -f single-filtered_allele_frequency.txt -t title -p 2 -o histogram
/share/nas1/pengzw/software/PloidyFrost/main/PloidyFrost-main/bin/PloidyFrost model -g single-filtered_allele_frequency.txt -l 1 -u 10 -q 0.05 -o gmm

根据文章中结果进行判断：