从SRA数据库上用prefetch下载文件

prefetch SRR14857120
![ISH}~5D@8@%K}6T.png

Fastq-dump解压

fastq-dump --split-files SRR14857120.sra(因开始所选基因组过大，下载太慢，所以换了个基因）

Q9N9Y(JW~X(FK2P5E02SK92.png

fastqc质控;去接头

fastqc SRR14857120_1.fastq

}Y9DMDEHB(I7{J}`POKG4(P.png

java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 ~/SRR14857120/SRR14857120_1.fastq ~/SRR14857120/SRR14857120_2.stq ./homework_out/output_forward_paired.fq.gz ./homework_out/output_forward_unpaired.fq.gz ./homework_out/output_reverse_paired.fq.gz ./homework_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75

ED(O$$K97_0$G74LKXWK@ER.png](https://upload-images.jianshu.io/upload_images/27142070-66cc1f2b2bf75ef8.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240) ![330F3670%V%6I3(_MVFC$W7.png

spades组装基因组草图

spades.py --careful --pe1-1 ~/SRR14857120/SRR14857120_1.fastq --pe1-2 ~/SRR14857120/SRR14857120_2.fastq -o ./homework__out

JZRGAJW$S9VH}1VMZ%X6NCD.png

quast评价组装的基因组效果

quast.py homework__out/contigs.fasta -o quast_out2
![RNA[{DX]IGGV.png](https://upload-images.jianshu.io/upload_images/27142070-08a4863dba3045a4.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240)
![GPQ4Q]Q[_D}1%KEY8YKF@4.png](https://upload-images.jianshu.io/upload_images/27142070-56f842cc37aa4a4f.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240) ![IVMCXWXR72F{Y(1TP2)M7ME.png](https://upload-images.jianshu.io/upload_images/27142070-a68bdd705a5da758.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240) ![%PG7BPCDTB8H0869B[_X({6.png](https://upload-images.jianshu.io/upload_images/27142070-25d0c54e7cfd999c.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240) ![8HJ$%@BZDIIRNRC[QTKA_AA.png](https://upload-images.jianshu.io/upload_images/27142070-7cd796f562594b88.png?imageMogr2/auto-orient/strip%7CimageView2/2/w/1240) ![9HMBUIXI@8)E6WD2U2@N2.png

G99AI48OBJ6RP0Y`KX7Z_3X.png