Bowtie2を使って、参照塩基配列と一致した配列を抽出、一致しなかった配列を抽出する ref: http://qiita.com/t_oginogin/items/3a890fd3fceaeff8a2d3

file0.txt

$ cd ~/research/
$ wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.2/bowtie2-2.2.2-linux-x86_64.zip
$ unzip bowtie2-2.2.2-linux-x86_64.zip

file1.txt

$ export PATH=~/research/bowtie2-2.2.2/:$PATH >> ~/.bashrc
$ source ~/.bashrc

file2.txt

$ cd ~/research/
$ wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
$ unzip hg19.zip -d indexes/

file3.txt

$ bowtie2-build reference.fasta ~/research/indexes/reference.fasta

file4.txt

$ bowtie2 -p 2 --un-conc target_nohg19.fastq --al-conc target_hg19.fastq -x ~/research/indexes/hg19 -1 target_1.fastq -2 target_2.fastq > /dev/null 2> target.log
$ cat target.log

file5.txt

$ bowtie2 -p 2 --un target_nohg19.fastq --al target_hg19.fastq -x ~/research/indexes/hg19 target.fastq > /dev/null 2> target.log
$ cat target.log