Uploading Data to SRA Using Aspera

TL;DR

Uploading data to SRA via HTTP or FTP is far too slow -- you will be waiting all day. The first time I tried uploading, the web interface never finished, and uploading files one by one via FTP was painful. Using Aspera made the experience much more comfortable. There is nothing complicated about it; it is essentially a faster version of scp.

In fact, looking at the NCBI page, Aspera Connect is recommended:

Aspera Connect Fast and Secure Protocol (FASP) uses User Datagram Protocol (UDP) that eliminates and overcomes many shortcomings of other FTP clients and we recommend it for all medium to large submissions and slow or unreliable connections (especially from abroad).

Installing Aspera Connect

Aspera Connect can be downloaded from IBM Aspera Connect. Below is an example for Linux. The version may be updated, so try to use the latest one.

wget https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect_4.0.2.38_linux.tar.gz

tar -zxvf ibm-aspera-connect_4.0.2.38_linux.tar.gz
bash ibm-aspera-connect_4.0.2.38_linux.sh

export PATH=$PATH:$HOME/.aspera/connect/bin

After adding it to your PATH, the ascp command becomes available. If needed, add it to ~/.profile or similar.

Uploading Files

An RSA Private Key will be displayed -- save it as ~/.aspera/keys/aspera_rsa. The FASTQ files you want to upload must be gzip-compressed. The upload destination uses a specified path that starts with your registered email address.

your_submission_directory="<[email protected]_xxxxx"

ascp -i ~/.aspera/keys/aspera_rsa -QT -l 100m -k1 -d path/to/your_reads.fastq.gz [email protected]:uploads/${your_submission_directory}