SRAtoolkit是NCBI开发的一个用于SRA文件处理的软件包，包含许多有用的工具。

下载SRAtoolkit软件包

软件包下载地址在NCBI网站：https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

目前最新版是2.10.8；有多个操作系统版本，我们选Ubuntu 64bit版；

  1. wget -P ~/download https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/sratoolkit.2.10.8-ubuntu64.tar.gz

解压压缩包

  1. tar zvxf ~/download/sratoolkit.2.10.8-ubuntu64.tar.gz -C ~/software
  2. mv ~/software/sratoolkit.2.10.8-ubuntu64 ~/software/sratoolkit

将sratoolkit安装文件路径加入环境变量

  1. echo "export PATH=$PATH:/home/ubuntu/software/sratoolkit/bin" >> ~/.zshrc
  2. source ~/.zshrc

使用fastq-dump和prefetch进行测试

更详细步骤和说明，参见官网Documentation：
https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=std

下载SRA文件

  1. prefetch SRR10107270
  2. 2020-10-03T06:03:13 prefetch.2.9.6: 1) Downloading 'SRR10107270'...
  3. 2020-10-03T06:03:13 prefetch.2.9.6:  Downloading via https...
  4. 2020-10-03T06:09:01 prefetch.2.9.6:  https download succeed
  5. 2020-10-03T06:09:01 prefetch.2.9.6: 1) 'SRR10107270' was downloaded successfully
  6. 2020-10-03T06:09:01 prefetch.2.9.6: 'SRR10107270' has 0 unresolved dependencies

解压SRA文件

  1. for i in *sra
  2. do
  3. echo $i
  4. fastq-dump --split-3 $i
  5. done

查看文件

  1. ls
  2. SRR10107270_1.fastq  SRR10107270_2.fastq  SRR10107270.sra
  1. head SRR10107270_1.fastq
  2. @SRR10107270.1 1 length=72
  3. TCGGGNAGTGCTAGCTCGCGATTCCAGGATGTAGTTAACCTTGAGCACAATTTCATTGACGNNAGCAGCNNN
  4. +SRR10107270.1 1 length=72
  5. AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE##EEEEEE###
  6. @SRR10107270.2 2 length=76
  7. CATGTNATTGTTGTAGGAATCAAAGTCAAACACATTTCGAACTACACTGGAGAGACCTTCANNCGGAAANTNNNGT
  8. +SRR10107270.2 2 length=76
  9. AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE/EEEEEE##EEEEEA#E###EE
  10. @SRR10107270.3 3 length=76
  11. AGACGNTGGAGGATGAAGGGCTGGCTGTTGGGTCTGTTCTTGCTCTAAGGCCACATCCTAGNAAAGCAGGGNNNGT

可以看到测序read的读长是七十多bp