trimmomatic修建二代数据

conda activate python2.7
trimmomatic PE -phred33 D2117372A_1.fq D2117372A_2.fq output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq-PE.all.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

只需更改D2117372A_1.fq D2117372A_2.fq双端测序文件

基因组survey

估算染色体倍数

conda activate python2.7

jellyfish count -C -m 21 -s 1000000000 -t 8 ~/geneomic/illumin/*.fq -o kmer_counts.jf

jellyfish histo kmer_counts.jf > kmer_k21.hist

conda activate r_env

Rscript ./genomescope.R kmer_k21.hist 21 200 ./genomescope

conda activate python3.10

L=$([smudgeplot.py](<http://smudgeplot.py/>) cutoff kmer_k21.hist L)

U=$([smudgeplot.py](<http://smudgeplot.py/>) cutoff kmer_k21.hist U)

jellyfish dump -c -L $L -U $U kmer_counts.jf | [smudgeplot.py](<http://smudgeplot.py/>) hetkmers -o kmer_pairs

smudgeplot.py plot kmer_pairs_coverages_2.tsv -o my_genome

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86%为二倍体

估算基因组大小

http://qb.cshl.edu/genomescope/

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结果分析：

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