To detect DNA fragments integration，such as T-DNA insertion，transgene integration

• Author rongzhengqin@basepedia.com

• bwa
• bamio (BasePedia internal code library)
• FragmentProcess（BasePedia internal code library）
• HomoFind (BasePedia internal code library)

snippet.bash

tar zxvf Insertsite-1.0.0.tar.gz
cd Insertsite-1.0.0
python setup.py build
python setup.py install

In linux bash sell, use followed script to execute.

snippet.bash

insertsite --hostgenome hostgenome.fa --targetgenome targetgenome.fa --fq1 sample.fq1.fq.gz --fq2 sample.fq2.fq.gz --libsize 500

• input instructions：
  • hostgenome - host genome fasta file
  • targetgenome - target genome fasta file
  • fq1 - sample 1st-end sequencing data
  • fq2 - sample 2nd-end sequencing data （Note：only support pair-end sequencing data）
  • libsize - library size