1. Quast安装

#预编译安装
tar zvxf /disk1/shares/quast-5.0.0.tar.gz -C ~/Biosofts/
#进入软件目录
cd Biosofts/quast-5.0.0/
#测试是否可以运行
./quast.py
#添加环境变量
echo 'export PATH=~/Biosofts/quast-5.0.0:$PATH' >> ~/.bashrc
source ~/.bashrc

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##也可尝试conda安装
 conda install -c bioconda quast

2.分别对Spades和velvet结果进行评价

python --version
## 如果你的python环境是3.8，则需要切换到python2环境
conda create --name python27 python=2.7 -y
conda activate python27

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#分别对SPAdes和velvet的拼接结果进行评价
quast.py velvet_out/contigs.fa -o quast_out1
## 如果出错，参考//www.greatytc.com/p/c8f265174570

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#查看quast_out1文件夹
ll quast_out1/
##从服务器下载该文件夹，打开html文件查看
#查看quast_out1
less quast_out1/report.txt

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#评价SPAdes拼接结果
quast.py SPAdesout/contigs.fasta -o quast_out2

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3. 比较spades和velvet拼接效果

#用Quast比较SPAdes和velvet的拼接结果
quast.py -o compare_spa_velvet velvet_out/contigs.fa SPAdesout/contigs.fasta

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4.比较error correction的重要性

#重新运行spades,without error correction
spades.py --only-assembler --careful --pe1-1 /disk1/shares/Seqs/test_7942raw_1.fq.gz --pe1-2 /disk1/shares/Seqs/test_7942raw_2.fq.gz -o ./SPAdesout_7942_new_without_correction

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#比较with和without error correction的SPAdes运行结果
quast.py -o compare_correction ./SPAdesout/contigs.fasta ./SPAdesout_7942_new_without_correction/contigs.fasta

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#重运行velvet:用SPAdes error correction之后的数据
velveth velvet_out_correction 31 -shortPaired -fastq -separate ./SPAdesout/corrected/test_7942raw_1.fq.00.0_0.cor.fastq.gz ./SPAdesout/corrected/test_7942raw_2.fq.00.0_0.cor.fastq.gz

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velvetg velvet_out_correction -exp_cov auto -cov_cutoff auto -very_clean yes

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#比较with和without error correction后的velvet运行结果
quast.py -o compare_velvet_correction ./velvet_out/contigs.fa ./velvet_out_correction/contigs.fa

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5. 比较不同km值拼接效果

quast.py -o compare_velvet_kmer velvet23/contigs.fa velvet31/contigs.fa velvet39/contigs.fa velvet47/contigs.fa velvet55/contigs.fa velvet63/contigs.fa velvet71/contigs.fa velvet79/contigs.fa velvet87/contigs.fa velvet95/contigs.fa velvet103/contigs.fa velvet111/contigs.fa velvet119/contigs.fa velvet127/contigs.fa

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