组装细菌基因组
1.上Genome Announcements网站(https://mra.asm.org/)找一篇细菌基因组文章;找到文章记载的SRA号;
2.从SRA数据库上用prefetch下载该文件
prefetch SRR14651518
3.Fastq-dump解压
fastq-dump --gzip --split-files SRR14651518
4.Fastqc质控
fastqc SRR14651518_1.fastq.gz
fastqc SRR14651518_2.fastq.gz
5.去接头
java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /disk/201931107010093/SRR14651518_1.fastq.gz /disk/201931107010093/SRR14651518_2.fastq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk/201931107010093/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75
spades.py --careful --pe1-1 /disk/201931107010093/trim_out/output_forward_paired.fq.gz --pe1-2 /disk/201931107010093/trim_out/output_reverse_paired.fq.gz -o ./work
7.Quast评价组装的基因组效果
quast.py work/work/contigs.fasta -o quast_SRR14651518