bioinfo

SRAtoolkit 安装与使用

Jeason

300字约1分钟

biosoftware

2019-10-13

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；

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

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

将sratoolkit安装文件路径加入环境变量

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

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

解压SRA文件

for i in *sra
do
echo $i
fastq-dump --split-3 $i
done

查看文件

ls
SRR10107270_1.fastq  SRR10107270_2.fastq  SRR10107270.sra

head SRR10107270_1.fastq
@SRR10107270.1 1 length=72
TCGGGNAGTGCTAGCTCGCGATTCCAGGATGTAGTTAACCTTGAGCACAATTTCATTGACGNNAGCAGCNNN
+SRR10107270.1 1 length=72
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE##EEEEEE###
@SRR10107270.2 2 length=76
CATGTNATTGTTGTAGGAATCAAAGTCAAACACATTTCGAACTACACTGGAGAGACCTTCANNCGGAAANTNNNGT
+SRR10107270.2 2 length=76
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE/EEEEEE##EEEEEA#E###EE
@SRR10107270.3 3 length=76
AGACGNTGGAGGATGAAGGGCTGGCTGTTGGGTCTGTTCTTGCTCTAAGGCCACATCCTAGNAAAGCAGGGNNNGT

可以看到测序read的读长是七十多bp