Why IBM Aspera?

IBM Aspera is utilised for file transfers at EMBL-EBI due to its ability to perform high-speed, secure transfers of large volumes of data, often outperforming protocols such as FTP or HTTP.
The core advantage is Aspera’s FASP protocol, which uses both TCP and UDP to optimise bandwidth usage, resulting in fast and reliable transfers without sacrificing security standards.

For other protocols, please check:

How to obtain credentials for EMBL-EBI?

To access and transfer files with IBM Aspera at EMBL-EBI, you require credentials. There are two account types:

Public Accounts: Obtainable via EMBL-EBI documentation, including a username and downloadable SSH key. Instructions are below in this document.
Private Accounts: Provided by ITS; more details can be found here: EMBL-EBI - Overview - Transfer Services (for EMBL-EBI members only).

You’ll use these credentials during setup, regardless of client or method.

Notable changes since last version

IBM Aspera Encryption Requirements at EMBL-EBI (2025 Update)

File transfer options

Option	Pros	Cons	Requirements
1) IBM Aspera Desktop Client	Easy to install and use Visual UI Monitor transfer speed and progress	GUI only (no CLI) No automation Requires a desktop environment (Linux)	macOS / Windows / Linux with GUI Username and password or SSH key Outbound TCP/UDP port 33001
2) IBM Aspera CLI (ascli) The new “standard” command-line client	Supports scripting and automation CLI browsing Retry support Works on many OS types (native or container) Pre-compiled binary available	Requires CLI and Ruby knowledge Set up more involved	Ruby 3.1+ ascli 4.22+ Credentials (password or SSH key) Outbound TCP/UDP port 33001
3) IBM Aspera Binary (ascp)	Lightweight and portable No installation needed Ideal for simple transfers	No browsing support No retry on failure Need to know file paths	Aspera SDK CLI access SSH key or password Outbound TCP/UDP port 33001
4) IBM Aspera Console/Orchestrator	Central management Set up workflows and automation Easy to use for teams	Requires licensed software Needs prior knowledge Not supported for public keys	Existing Aspera HSTS license Console or Orchestrator installed Private account (RSA key or password) Outbound TCP/UDP port 33001

Option 1 - IBM Aspera Desktop client

The free IBM Aspera for Desktop application is the new client which replaced the Desktop Client in December 2024.

Typical installation steps

Download the free IBM Aspera for Desktop client here: Aspera for desktop - IBM Aspera on Cloud
Install the client. You can find documentation here: Getting started - IBM Documentation
Start the IBM Aspera for Desktop client and create a new connection to an EMBL-EBI server:

Click Link Account
Select IBM Aspera HSTS, give it a display name, and then toggle Use transfer user. Enter the name of the EMBL-EBI Aspera server: fasp.ebi.ac.uk Enter the username, for example: fasp-public
You will now need to also enter the password for your username or provide a private SSH key. If you are using a public account, you must use a specific key, which you can find in the instructions below in this same document An EMBL-EBI member will provide you with a username/password or SSH key if you are using a private account. EMBL-EBI members can find how to manage Transfer accounts in the internal documentation EMBL-EBI - Overview - Transfer Services (for EMBL-EBI members only). To add your key, select Choose file to import it. Click Link to finish setting up your transfer account.
You should now see the account you added (similar to the example on the right)
To view files available on the server, double-click on the account. Browse to the files or folders you wish to download, and select Download.
Click the transfer monitor icon to check the status of your transfer.

Option 2 - Command line client (ASCLI)

Typical installation steps

Choose one of the following methods:
1. Install ascli with instructions from here: IBM/aspera-cli: IBM Aspera CLI (github.com)
2. Download a pre-built executables here: Index of /download/aspera-cli/

Check you can run them:

Linux

$ wget https://eudemo.asperademo.com/download/aspera-cli/ascli.4.23.0.linux-x86_64.gblic_2.30
$ mv ascli.4.23.0.linux-x86_64.gblic_2.30 ascli
$ chmod u+x ascli
$ ldd ./ascli
        linux-vdso.so.1 (0x00007ffd56b58000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f151af3c000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f151af37000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f151ae5c000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f151ac00000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f151af4c000)
$ ./ascli -v
4.23.0
$

MacOS

$ wget https://eudemo.asperademo.com/download/aspera-cli/ascli.4.21.1.osx-arm64
$ mv ascli.4.21.1.osx-arm64 ascli
$ chmod +x ascli
$ xattr -dr com.apple.quarantine ./ascli   # first run on macOS
$ ./ascli -v

For both options, you must ensure you have installed ascp:

https://www.ibm.com/products/aspera/downloads

GitHub - IBM/aspera-cli: IBM Aspera CLI

ascli conf ascp install
 Time: 00:00:00 ================================ 100% 0 Mbps Time: 00:00:00
Installed IBM Aspera Transfer SDK version 1.1.6

Test your credentials:
1. If you are using a public account, you must download the private SSH key. Instructions on how to do this can be found in the section below(Public RSA PRIVATE KEY SSH key for use with EMBL-EBI Aspera public account IBM Aspera transfers).
2. If you are using a private account, an EMBL-EBI member will provide you with a username/password or username/SSH key.
  1. EMBL-EBI members can find how to manage Transfer accounts in the internal documentation=> EMBL-EBI - Overview - Transfer Services (for EMBL-EBI members only).

You must now create an option preset, which is a configuration template to connect to the EMBL-EBI Aspera transfer server: https://github.com/IBM/aspera-cli?tab=readme-ov-file#quick-start

With username/password:

ascli config preset update ebi --ssh-options=@json:'{"use_agent": false}' --url=ssh://fasp.ebi.ac.uk:33001 --username=username --password=my_password_here

With username/SSH key: (Public key can be found in another section of this documentation)

ascli config preset update ebi --ssh-options=@json:'{"use_agent": false}' --url=ssh://fasp.ebi.ac.uk:33001 --username=myusername --ssh-keys=/path-to-private-ssh-key

This will create a preset called “ebi” for ascli.
You can set this preset to be the default:

ascli config preset set default server ebi

If you have only one preset, setting it as the default is convenient.
If you want to use multiple presets, you specify the preset name - see below:

Testing the connection

You can test the connection to the server like this:

$ ascli server --preset=ebi browse /   # This specifies the preset
$ ascli server browse /          # This uses the default preset

This will browse the / root of the folder you have access to on the Aspera server.
If you get the error “ERROR -- net.ssh.authentication.agent: could not connect to ssh-agent: Agent not configured", see GitHub - IBM/aspera-cli: IBM Aspera CLI

$ ascli server --ssh-options=@json:'{"use_agent": false}'

Usage examples:

Browse the top-level directory and browse a subdirectory:

ascli server browse /
[this displays top level directory you have access to, for example:]
│ zmode      │ zuid │ zgid    │ size │ mtime                     │ name           │
╞════════════╪══════╪═════════╪══════╪═══════════════════════════╪════════════════╡
│ drwxr-xr-x │ root │ root    │ 29   │ 2023-10-25 09:39:52 +0100 │ biostudies     │
│ drwxr-xr-x │ root │ root    │ 17   │ 2025-06-23 11:33:22 +0100 │ ensemblgenomes │
│ drwxr-xr-x │ root │ root    │ 17   │ 2025-07-02 09:47:51 +0100 │ ensemblorg     │

To browse to a subdirectory:
ascli server --preset=ebi browse /1000g
Output:
 zmode      │ zuid │ zgid │ size │ mtime                     │ name             │
╞════════════╪══════╪══════╪══════╪═══════════════════════════╪══════════════════╡
│ -rw-r--r-- │ root │ root │ 39   │ 2009-02-27 17:36:40 +0000 │ .welcome         │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-07-06 02:01:31 +0100 │ ftp              │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-07-06 02:01:31 +0100 │ nfs              │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-07-06 02:01:31 +0100 │ test             │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-07-06 02:01:31 +0100 │ test2            │
│ -rw-r--r-- │ root │ root │ 0    │ 2024-06-11 09:33:23 +0100 │ test_staging.txt │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-07-06 02:01:31 +0100 │ withdrawn        │

You can now browse into the subdirectory you are interested in, for example:
ascli server --preset=ebi browse /1000g/test/data/NA12282/sequence_read

Download directory:

ascli server --preset=ebi download --ts=@json:'{"resume_policy":"sparse_csum"}' /1000g/test/data/NA12282/sequence_read

Download individual file:

ascli server --preset=ebi download --ts=@json:'{"resume_policy":"sparse_csum"}' /1000g/test/data/NA12282/sequence_read/SRR015389.recal.fastq.gz

Full example with a standard public user

Public archive about downloading public data

### Get the private key and 0600

root@jmr ~/aspera # echo '-----BEGIN RSA PRIVATE KEY-----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-----END RSA PRIVATE KEY-----' > public_accounts_rsa_sha2_256_keypair/id_rsa_ebi_public.key

root@jmr ~/aspera # chmod 0600 public_accounts_rsa_sha2_256_keypair/id_rsa_ebi_public.key

### Get the binary, and make it executable

root@jmr ~/aspera # curl https://eudemo.asperademo.com/download/aspera-cli/ascli.4.24.1.linux-x86_64.gblic_2.30 --output ascli.4.24
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 27.6M  100 27.6M    0     0  60.6M      0 --:--:-- --:--:-- --:--:-- 60.6M

root@jmr ~/aspera # chmod u+x ascli.4.24

### Declare the preset

root@jmr ~/aspera # ./ascli.4.24 config preset update public-ebi --ssh-options=@json:'{"use_agent": false}' --url=ssh://fasp.ebi.ac.uk:33001 --username=fasp-public --ssh-keys=public_accounts_rsa_sha2_256_keypair/id_rsa_ebi_public.key
Updated: public-ebi
Saving config file.

### List folders

root@jmr ~/aspera # ./ascli.4.24 --preset=public-ebi server browse /
╭────────────┬──────┬─────────┬──────┬───────────────────────────┬────────────────╮
│ zmode      │ zuid │ zgid    │ size │ mtime                     │ name           │
╞════════════╪══════╪═════════╪══════╪═══════════════════════════╪════════════════╡
│ drwxr-xr-x │ root │ root    │ 18   │ 2025-07-25 17:50:15 +0200 │ biostudies     │
│ drwxr-xr-x │ root │ root    │ 17   │ 2025-06-23 12:33:22 +0200 │ ensemblgenomes │
│ drwxr-xr-x │ root │ root    │ 17   │ 2025-07-02 10:47:51 +0200 │ ensemblorg     │
│ drwxr-xr-x │ root │ gendata │ 651  │ 2025-06-25 16:22:31 +0200 │ pub            │
│ drwxr-xr-x │ root │ root    │ 4096 │ 2025-11-16 03:03:36 +0100 │ 1000g          │
│ drwxr-xr-x │ root │ root    │ 32   │ 2023-10-25 10:39:55 +0200 │ empiar         │
│ drwxr-xr-x │ root │ root    │ 4096 │ 2025-11-16 03:03:36 +0100 │ faang          │
│ drwxr-xr-x │ root │ root    │ 4096 │ 2025-11-16 03:03:36 +0100 │ hipsci         │
│ drwxr-xr-x │ root │ root    │ 4096 │ 2025-11-16 03:03:36 +0100 │ pride-archive  │
│ drwxr-xr-x │ root │ root    │ 18   │ 2023-10-25 10:40:06 +0200 │ pride          │
│ drwxr-xr-x │ root │ root    │ 4096 │ 2025-11-16 03:03:36 +0100 │ vol1           │
╰────────────┴──────┴─────────┴──────┴───────────────────────────┴────────────────╯

root@jmr ~/aspera # ./ascli.4.24 --preset=public-ebi server browse /1000g
╭────────────┬──────┬──────┬──────┬───────────────────────────┬──────────────────╮
│ zmode      │ zuid │ zgid │ size │ mtime                     │ name             │
╞════════════╪══════╪══════╪══════╪═══════════════════════════╪══════════════════╡
│ -rw-r--r-- │ root │ root │ 39   │ 2009-02-27 18:36:40 +0100 │ .welcome         │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-11-16 03:03:36 +0100 │ ftp              │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-11-16 03:03:36 +0100 │ nfs              │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-11-16 03:03:36 +0100 │ test             │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-11-16 03:03:36 +0100 │ test2            │
│ -rw-r--r-- │ root │ root │ 0    │ 2024-06-11 10:33:23 +0200 │ test_staging.txt │
│ drwxr-xr-x │ root │ root │ 4096 │ 2025-11-16 03:03:36 +0100 │ withdrawn        │
╰────────────┴──────┴──────┴──────┴───────────────────────────┴──────────────────╯

### Download the file - FAILURE
root@jmr ~/aspera # ./ascli.4.24 --preset=public-ebi server download /1000g/.welcome
ERROR: Other(RuntimeError): no Aspera transfer module or SDK found.-=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=---=-- 0% 0 Mbps  ETA: ??:??:??
Refer to the manual or install SDK with command:
ascli conf ascp install
Use --log-level=debug to get more details.

### Install the internal dependency

root@jmr ~/aspera # ./ascli.4.24 conf ascp install
 Time: 00:00:00 ===================================================================================================================================================================================================================================== 100% 0 Mbps Time: 00:00:00
Installed IBM Aspera Transfer SDK version 1.1.6

### Download the file SUCCESS

root@jmr ~/aspera # ./ascli.4.24 --preset=public-ebi server download /1000g/.welcome
 Time: 00:00:01 ===================================================================================================================================================================================================================================== 100% 0 Mbps Time: 00:00:01

### Read the local file 

root@jmr ~/aspera # head .welcome

 ftp.1000genomes.ebi.ac.uk FTP server
root@jmr ~/aspera #

Option 3 - Binary (ascp)

Typical usage

Export credentials to an environment variable.
Run ascp with necessary flags for upload/download:

Download the Aspera Transfer SDK from the following link: Aspera Transfer SDK - IBM API Hub - IBM Developer
Unzip/untar into a suitable directory, for example, C:\aspera on Windows or /opt/aspera on Linux
If you are using a public EMBL-EBI account, you must download the private SSH key. Instructions on how to do this can be found in the document below.
You can ignore most of the directories that the SDK writes to your machine.
1. Please navigate to the /aspera/bin directory. This is the location where you will find the ascp binary. This directory is the one you will use to initiate Aspera transfers.
2. You can now simply execute ascp to start your transfer with the EMBL-EBI server.
  1. Basic syntax:
    1. Upload with username/password:
```
./ascp -Q -l 300M filename/dir myusername@fasp.ebi.ac.uk:
```
    2. Download with username/password:
```
./ascp -Q -l 300M myusername@fasp.ebi.ac.uk:/source_dir .
```
Transferring with a password for the EMBL-EBI server:

We recommend setting your password as an environment variable in your shell. This way, you won't have to type it in each time.

Linux/OSX:

export ASPERA_SCP_PASS=mypassword

Windows:

set ASPERA_SCP_PASS=mypassword

Transferring with an SSH key:

./ascp -Q -l 300M -i /path_to_private_key myusername@fasp.ebi.ac.uk:/source_dir .

Further ascp examples are here: Ascp command reference - IBM Documentation

Option 4 - Use your own licensed Aspera applications

Typical Usage

Add EBI as an Unmanaged Node in the Console.
Create an endpoint and apply credentials.
Initiate transfers through the Console or automate them with Orchestrator’s workflow plugins.

You may already have a licensed IBM Aspera High Speed Transfer Server.
You can use your existing transfer application to transfer files with the IBM Aspera High-Speed Transfer Server at EBI.
You can use your existing IBM Aspera software with any of the options listed above.
Additionally, you should be licensed for applications that can initiate transfers through a web application, such as Aspera Console or Aspera Orchestrator.

Steps with the Aspera console

Add the EBI Aspera server as an Unmanaged Node in Aspera Console: Adding Unmanaged Nodes - IBM Documentation
For your new unmanaged EMBL-EBI node, create a new endpoint: Adding Endpoints - IBM Documentation
- You will need your credentials for your endpoint.
  - These would be username/password or username/SSH key.
  - Please note that transferring with Console and the SSH key for public EMBL-EBI accounts is not supported.
  - Only transfers for private accounts with RSA SSH keys are supported. Transferring Files with an Endpoint Using SSH Keys - IBM Documentation
Create a new Smart Transfer: Creating a Smart Transfer - IBM Documentation

Steps with Aspera Orchestrator

In Orchestrator, create a new remote node: Creating a Remote Node - IBM Documentation
Create a new workflow with the Aspera node API transfer plugin.
- Note that you must configure the workflow to always initiate the connection from your transfer server to the EMBL-EBI server.

Public RSA PRIVATE KEY SSH key for use with EMBL-EBI Aspera public account IBM Aspera transfers

To use IBM Aspera for downloading public data from EMBL-EBI, you will need the correct private SSH key for authentication.

If you have a private account, you will not use this key; instead, you will log on with your username and password.

The key is available for download here: [LINK] and also below:

You must save this key to your own machine, with permissions 0600 .

You can use this SSH key to log in with the fasp-public account using any of the applications listed above.

Versions

You must have a newer version of the Aspera software for use with this key and the public accounts.

The ascp version must be 4.4.4 or newer. You must upgrade if you have an older version.

Aspera Connect(Aspera Connect will be End of Life June 2026. Please use IBM Aspera for Desktop instead.)	4.2.7
IBM Aspera for Desktop	1.0.6
Transfer SDK	1.1.6
HSTS/Endpoint	4.4.4
ascli	4.23.0

Troubleshooting

Ensure the firewall allows outbound TCP/UDP port 33001 to the EMBL‑EBI endpoint IP (e.g. 193.62.193.164). Updated network information should be in the EMBL-EBI Public data access documentation
Error: "could not load key" often means an incorrect path or file.
If you get "ssh authentication failed", check that you have specified the full path to your key with -i, and the key is only readable by your user (600)
If you are prompted for a password something is wrong with your key authentication, please check the permissions and your syntax.

Testing Login from the command-line

ascp (command-line)	`$ ascp -L- -P 33001 --mode=test-login -i [path_to_key] fasp-public@fasp.ebi.ac.uk` You should see: LOG [asssh] test login succeeded, exiting.
Aspera Connect	See ascp above
IBM Aspera for Desktop	After installing, you should have ascp in your path See ascp above.
ascli	Test with the ascp that comes with the IBM Aspera Transfer SDK - IBM API Hub - IBM Developer See above for the method
Transfer SDK	If you have downloaded the IBM Aspera Transfer SDK - IBM API Hub - IBM Developer You will have the ascp binary in the /bin folder - test with the ascp command above
HSTS/Endpoint	See ascp above

Example ascp command-line transfer using the SSH key

$ ascp -Q -l 300m -P33001 -i /path/to/key era-fasp@fasp.sra.ebi.ac.uk:/remote/path/file.fastq.gz /local/destination/

For Windows, remember to put directories with spaces in " " double quotes.

How to transfer files to and from EMBL-EBI using IBM Aspera

Table of Contents

Why IBM Aspera?

How to obtain credentials for EMBL-EBI?

Notable changes since last version

File transfer options

Option 1 - IBM Aspera Desktop client

Typical installation steps

Option 2 - Command line client (ASCLI)

Typical installation steps

Testing the connection

Usage examples:

Browse the top-level directory and browse a subdirectory:

Download directory:

Download individual file:

Full example with a standard public user

Option 3 - Binary (ascp)

Typical usage

Option 4 - Use your own licensed Aspera applications

Typical Usage

Steps with the Aspera console

Steps with Aspera Orchestrator

Public RSA PRIVATE KEY SSH key for use with EMBL-EBI Aspera public account IBM Aspera transfers

Versions

Troubleshooting

Testing Login from the command-line

Example ascp command-line transfer using the SSH key