工欲善其事必先利其器
ascp(Aspera Command Line Transfer)是一种用于高速数据传输的命令行工具,由 Aspera 开发,用于在网络上传输大型数据集和文件。它专为大容量、高速度和安全性而设计,适用于远程文件传输,特别是在需要高效传输大量数据的情况下。
主要特点和功能:
官网:https://www.ibm.com/products/aspera/downloads?list
一般推荐使用Conda安装管理软件
conda install -c hcc aspera-cli -y
#检查ascp是否下载成功
ascp -h
从NCBI-SRA下载accession list,把SRA编号,通过vim写到SRA.list里
使用ascp下载需要密匙asperaweb_id_dsa.openssh,位置在:
#我的环境名称是chip,文件路径需要自行探索:
#miniconda3/envs/chip/etc/asperaweb_id_dsa.openssh
#单端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
echo $id
ascp -QT -l 300m -P33001 -i \
$HOME/miniconda3/envs/chip/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/$id/${id}.fastq.gz ./
done
#双端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
echo $id
ascp -QT -l 500m -P33001 -i \
$HOME/miniconda3/envs/rna/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/$id/${id}_1.fastq.gz \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/$id/${id}_2.fastq.gz ./
done
#单端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
y=$(echo $id | cut -b10-10)
echo $id
ascp -QT -l 300m -P33001 -i \
$HOME/miniconda3/envs/chip/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/00$y/$id/${id}.fastq.gz ./
done
#双端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
y=$(echo $id | cut -b10-10)
echo $id
ascp -QT -l 500m -P33001 -i \
$HOME/miniconda3/envs/rna/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/00$y/$id/${id}_1.fastq.gz \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/00$y/$id/${id}_2.fastq.gz ./
done
#单端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
y=$(echo $id | cut -b10-11)
echo $id
ascp -QT -l 300m -P33001 -i \
$HOME/miniconda3/envs/chip/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/0$y/$id/${id}.fastq.gz ./
done
#双端测序:
cat SRA.list|while read id
do
x=$(echo $id | cut -b1-6)
y=$(echo $id | cut -b10-11)
echo $id
ascp -QT -l 500m -P33001 -i \
$HOME/miniconda3/envs/rna/etc/asperaweb_id_dsa.openssh \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/0$y/$id/${id}_1.fastq.gz \
era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/$x/0$y/$id/${id}_2.fastq.gz ./
done
下载后直接是fastq,不用转换格式
其实不管单双端,SRR六七八位数,就是根据url地址找规律......