組裝

分別使用Canu,Flye, Ra, Shasta組裝ecoli k-12 標準菌株並製作完整組裝報告

菌株位置：

/bip5_disk/peiwen107/medaka_alignment/ecoli/Ecoli_1.5G.fastq

• Step1. Run abyss-fac for raw read

• Step2. Run fastqc

  /bip6_disk/shiuanrung107/fastqc/FastQC/fastqc /bip5_disk/peiwen107/medaka_alignment/ecoli/Ecoli_1.5G.fastq
  

• Step3. Run Assembler (要計算時間)

  /usr/bin/time -o time.txt -p nohup yourcommand &
  

• Step4. Analysis result

  1. run blast
  2. run bandage for contig status
  3. run abyss-fac for contig

• Step5. 製作ppt

寫一個python 程式計算gc content

• Step1. 至ncbi 抓取菌株

• Step2. 程式步驟

  1. 讀入fasta檔
  2. 計算sequence的gc content 可使用(SeqIO做序列處理)

  3. 執行程式必須為此方式

     > python yourpyscript.py  ecoli.fasta
     output : 
     	gc-content: XX.X%
     

     hint1:
     import sys
     with open(sys.argv[1],'r') as f:
     

     hint2:
     import sys
     from Bio import SeqIO
     record = SeqIO.read(sys.argv[1], "fasta")