本方法仅供个人使用！！
# 进入conda环境
conda activate genome_feature
# 安装
conda install -c bioconda quast运行 quast.py
mkdir quast && cd quast
# NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
# WARNING: GeneMark tool can't be started because of license limitations!
# so 选择--glimmer
quast.py ../3.15188_genome.fasta --fungus --glimmer -t 8 -o 3.15188
QUAST结果
# 结果文件
report.txt summary table
report.tsv tab-separated version, for parsing, or for spreadsheets (Google Docs, Excel, etc)
report.tex Latex version
report.pdf PDF version, includes all tables and plots for some statistics
report.html everything in an interactive HTML file
icarus.html Icarus main menu with links to interactive viewers
contigs_reports [only if a reference genome is provided]
misassemblies_report detailed report on misassemblies
unaligned_report detailed report on unaligned and partially unaligned contigs
k_mer_stats [only if --k-mer-stats is specified]
kmers_report detailed report on k-mer-based metrics
reads_stats [only if reads are provided]
reads_report detailed report on mapped reads statistics看report.html网页结果全面，会有图和数据，report.txt则是主要数据。
# 得到如下重要内容
# contigs 16
Largest contig 4508325
Total length 34000033
GC (%) 48.49
N50 3074509
N90 1550349
auN 2916380.1
L50 5
L90 12
批量运行
# pep70
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/70list.txt`
do
echo "quast.py /media/aa/DATA/SZQ2/bj/a.preparing_data/genome_unmasked_fasta_data/$i.genome.fasta --fungus --glimmer -t 8 -o $i"
done > command.quast.list
ParaFly -c command.quast.list -CPU 48
# pepmy
for i in `cat /media/aa/DATA/SZQ2/bj/functional_annotation/pepmylist.txt`
do
echo "quast.py /media/aa/DATA/SZQ2/bj/a.preparing_data/genome_unmasked_fasta_data/$i.genome.fasta --fungus --glimmer -t 8 -o $i"
done > command.quast2.list
ParaFly -c command.quast2.list -CPU 48