ART的安装和简单使用

安装环境

Ubuntu18.10
ART-bin-MountRainier-2016.06.05-Linux64

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安装过程

1、从ART - Set of Simulation Tools下载安装包。  
https://www.niehs.nih.gov/research/resources/assets/docs/artbinmountrainier2016.06.05linux64.tgz
2将安装包sudo mv artbinmountrainier2016.06.05linux64.tgz -t /opt

3.然后

cd /opt
tar xzvf artbinmountrainier2016.06.05linux64.tgz
echo "export PATH=\$PATH:/opt/art_bin_MountRainier" >> ~/.bashrc
source ~/.bashrc
art_illumina

这里就安装完毕了。

简单试用

输入14kB模拟数据example.fa

art_illumina -ss HS25 -i ./example.fa -o ./paired_end_com -l 150 -f 10 -p -m 500 -s 10 -sam

控制台输出结果为

ubuntu@VM-16-5-ubuntu:~$ art_illumina -ss HS25 -i ./example.fa -o ./paired_end_com -l 150 -f 10 -p -m 500 -s 10 -sam

    ====================ART====================
             ART_Illumina (2008-2016)
          Q Version 2.5.8 (June 7, 2016)
     Contact: Weichun Huang <whduke@gmail.com>
    -------------------------------------------

                  Paired-end sequencing simulation

Total CPU time used: 0.01

The random seed for the run: 1637467638

Parameters used during run
        Read Length:    150
        Genome masking 'N' cutoff frequency:    1 in 150
        Fold Coverage:            10X
        Mean Fragment Length:     500
        Standard Deviation:       10
        Profile Type:             Combined
        ID Tag:

Quality Profile(s)
        First Read:   HiSeq 2500 Length 150 R1 (built-in profile)
        First Read:   HiSeq 2500 Length 150 R2 (built-in profile)

Output files

  FASTQ Sequence Files:
         the 1st reads: ./paired_end_com1.fq
         the 2nd reads: ./paired_end_com2.fq

  ALN Alignment Files:
         the 1st reads: ./paired_end_com1.aln
         the 2nd reads: ./paired_end_com2.aln

  SAM Alignment File:
        ./paired_end_com.sam

输出文件如下：

 

art_illumina_result.png