Upload Guide

Overview

This guide provides instructions for securely uploading genomic data files to IntelliSeq's FTPS (FTP over SSL/TLS) server. IntelliSeq, a leading Polish bioinformatics company specializing in automated genomic data analysis, uses secure FTPS to ensure the confidentiality and integrity of your sensitive genetic data during transfer.

Connection Details

• Server Address: ftps.intelliseq.com

• Port:

  • 21 (FTP with explicit TLS/SSL)

  • 990 (Implicit FTPS)

• Protocol: FTPS (FTP over SSL/TLS)

• Encryption: Required (TLS/SSL)

• Username: Contact your IntelliSeq representative

• Password: Contact your IntelliSeq representative

Important: Your login credentials are unique to your organization. Please contact your IntelliSeq representative to obtain your username and password.

Method 1: FileZilla (Recommended for Most Users)

FileZilla is a free, user-friendly FTP client with excellent FTPS support.

Installation

1. Download FileZilla from https://filezilla-project.org/

2. Install FileZilla following the installation wizard

Configuration

1. Open FileZilla

2. Click File → Site Manager

3. Click New Site and name it "IntelliSeq FTPS"

4. Configure the following settings:

   • Protocol: FTP - File Transfer Protocol

   • Host: ftps.intelliseq.com

   • Port: 21

   • Encryption: Require explicit FTP over TLS

   • Logon Type: Normal

   • User: Your provided username

   • Password: Your provided password

5. Click Connect

Uploading Files

1. In the left panel (Local site), navigate to your files

2. In the right panel (Remote site), you'll see your home directory

3. Drag and drop files from left to right to upload

4. Monitor the transfer progress in the bottom panel

Method 2: Command Line (Linux/macOS)

Using lftp

lftp is a sophisticated command-line FTP client with robust FTPS support.

Installation

# Ubuntu/Debian
sudo apt-get install lftp

# macOS (with Homebrew)
brew install lftp

# RHEL/CentOS
sudo yum install lftp

Basic Usage

# Connect to the server
lftp -u YOUR_USERNAME ftps://ftps.intelliseq.com:21

# After entering password, upload a file
put /path/to/your/file.fastq.gz

# Upload multiple files
mput *.fastq.gz

# Upload entire directory
mirror -R /path/to/local/directory /remote/directory

# Exit
quit

Batch Upload Script

Create a script for automated uploads:

#!/bin/bash
# upload_to_intelliseq.sh

lftp -u YOUR_USERNAME,YOUR_PASSWORD ftps://ftps.intelliseq.com:21 <<EOF
set ssl:verify-certificate no
cd /
mput /path/to/files/*.fastq.gz
quit
EOF

Method 3: Using curl

curl can be used for simple file uploads via FTPS.

Single File Upload

curl -T /path/to/file.fastq.gz \
     --ftp-ssl \
     --user YOUR_USERNAME:YOUR_PASSWORD \
     ftp://ftps.intelliseq.com/file.fastq.gz

Upload with Progress Bar

curl -T /path/to/file.fastq.gz \
     --ftp-ssl \
     --user YOUR_USERNAME:YOUR_PASSWORD \
     --progress-bar \
     ftp://ftps.intelliseq.com/file.fastq.gz

Upload Multiple Files

for file in *.fastq.gz; do
    curl -T "$file" \
         --ftp-ssl \
         --user YOUR_USERNAME:YOUR_PASSWORD \
         ftp://ftps.intelliseq.com/"$file"
done

Method 4: Python Script

For programmatic uploads, you can use Python:

import ftplib
import os
import ssl

def upload_to_intelliseq(local_file, remote_file, username, password):
    """Upload a file to IntelliSeq FTPS server"""
    
    # Create SSL context
    context = ssl.create_default_context()
    
    # Connect to FTPS server
    ftps = ftplib.FTP_TLS(context=context)
    ftps.connect('ftps.intelliseq.com', 21)
    
    # Login
    ftps.login(username, password)
    
    # Switch to secure data connection
    ftps.prot_p()
    
    # Upload file
    with open(local_file, 'rb') as file:
        ftps.storbinary(f'STOR {remote_file}', file)
    
    # Close connection
    ftps.quit()
    
    print(f"Successfully uploaded {local_file}")

# Example usage
upload_to_intelliseq('sample.fastq.gz', 'sample.fastq.gz', 'YOUR_USERNAME', 'YOUR_PASSWORD')

File Types and Naming Conventions

IntelliSeq accepts various genomic data formats:

• FASTQ files: .fastq, .fastq.gz, .fq, .fq.gz

• BAM/SAM files: .bam, .sam

• VCF files: .vcf, .vcf.gz

• BED files: .bed

Recommended Naming Convention

[SampleID]_[FlowcellID]_[Lane]_[Read]_[Number].fastq.gz

Example: PATIENT001_HXXXXX_L001_R1_001.fastq.gz

Security Best Practices

1. Always use FTPS (never plain FTP) to ensure data encryption

2. Verify the server certificate when prompted

3. Do not share your credentials with unauthorized persons

4. Use strong passwords and change them regularly

5. Log out properly after completing uploads

Troubleshooting

Connection Issues

Problem: Cannot connect to server

• Verify your internet connection

• Check if your firewall allows connections on ports 21 and 990

• Ensure passive mode ports (10090-10100) are not blocked

Problem: Authentication failed

• Verify username and password with IntelliSeq support

• Check for extra spaces in credentials

• Ensure CAPS LOCK is off

Transfer Issues

Problem: Uploads failing or timing out

• Check file permissions on local system

• Verify sufficient storage space

• Try uploading smaller files first

• Use passive mode if behind a firewall

Problem: Slow upload speeds

• Compress files before uploading (.gz format)

• Upload during off-peak hours

• Check your internet upload bandwidth

Certificate Warnings

If you receive SSL certificate warnings:

1. Verify the certificate is for ftps.intelliseq.com

2. Accept the certificate if valid

3. Contact IntelliSeq support if concerns persist

Support

For technical assistance or questions:

• Email: [email protected]

• Documentation: Visit intelliseq.com

Data Processing

Once your files are successfully uploaded:

1. IntelliSeq's automated iFlow™ platform begins processing

2. You'll receive email notifications about processing status

3. Results will be available through your IntelliSeq portal

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Last updated: January 2025 IntelliSeq - Advancing Genomic Analysis Through Innovation