FAQ

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GETTING STARTED

Click LOGIN at the upper right corner of alapy.com website to be redirected to the AGx. You can start using it right away. However, functionality is limited until you register. Please JOIN PIONEERS to get your full access login_full
Please register to get access to the full functionality of AGx.
You can click JOIN PIONEERS button in the upper right corner of alapy.com website to register.
register1
You will be redirected to the registration form. After you filled in the form you may choose between registering with Google account (click blue GOOGLE button) or by creating login and password (click blue LOGIN/PASSWORD button). These buttons are going to become clickable only when the "I have read and agree to the Terms of Service" checkbox is selected.
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If you select LOGIN/PASSWORD, your email is going to be your login. Please type in and re-type password you want to use for authentication. After this, we will send you a confirmation email about your registration.
If you select GOOGLE, we will send you a confirmation email that you registered right away.
Once you registered, our specialists will look at your form and grant authentication to use AGx. Congratulations, now you can begin using ALAPY Genome Explorer! Thank you,
ALAPY team
To use the app’s full function range, one needs to log in. To undergo authentication, user needs to push the Login button in the top right hand corner. The app supports 2 authentication types:
  • Classic authentication using a login and a password.
  • Authentication via a Google account.
The preferred type should be selected dependent on the registration type. For authentication using login/password one needs to type their email address in the login field, and type the password provided during the registration in the password field. Then user should tap LOGIN.
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Authentication via a Google account requires tapping the GOOGLE ACCOUNT button. Then you’ll be redirected to the Google authentication page.

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MAKE ANALYSIS

Sample uploading is only available to authorized users. To upload a sample, a user needs to tap the Samples button in the app’s top left-hand corner.
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Then, the sample uploading window can be observed.
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To upload a sample one needs to click the uploading area inside the window.
Then the system will offer to select a file to upload.
Currently, AGx is optimized to upload multisample vcf and vcf.gz files from whole exome sequencing experiments and gene panel NGS experiments. In order to upload vcf files with millions of positions, we recommend integrating AGx with your system for direct upload and with built-in filtration for genic and regulatory regions in order to increase productivity.
After a file has been selected, the user needs to press the Upload button in the bottom left-hand corner. After pressing the Upload button, sample uploading and processing process will launch. During the upload process, the sample file is sorted, parsed into the database, indexes created, genotype processed to derive zygosity and first comparison with RefSeq is created to predict mutations consequences. The uploading process is displayed in the uploading bar. Approximate sample uploading time is 2 minutes.
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After uploading the sample, its metadata can be filled in by clicking the EDIT button under it.
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To search for a sample using its name and metadata, a full text search option has been implemented.
sample_metadata_search
To conduct analysis, the user needs to push the Analysis button in the app’s top left-hand corner.
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Upon pushing, the analysis window will open.
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Currently, there are 3 analysis types are available in the system:
      • Single
      • Tumor/Normal
      • Family
In the menu on the left, your analysis history is available. To look for the analyses conducted, you can use the full-text search bar, that includes search in the Description field of the analysis.
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When a conducted analysis is tapped, you can view its data and restore the results by pressing view results button.
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UNIX BASIC COMMANDS AND USAGE EXAMPLES

To compress your fastq or fastq.gz file to ALAPY Compression format .ac file use option -c or --compress like so:

alapy_arc -c your_file.fastq
alapy_arc -c your_file.fastq.gz
alapy_arc --compress your_file.fastq
alapy_arc --compress your_file.fastq.gz

This will create your_file.ac file in the same directory as your original file unless you used option to change output directory (-o --outdir) or to change output file name (-n --name).

If you already have a file with output file name in place than version extension will be added
To decompress a .ac file of ALAPY Compression format to .fastq file use option -d or --decompress like so:

alapy_arc -d your_file.ac
alapy_arc --decompress your_file.ac

This will decompress the file in the same directory into your_file.fastq.gz file unless you used option to change output directory (-o --outdir) or to change output file name (-n --name).

If you already have a file with output file name in place than version extension will be added
Create all output files in the specified output directory using -o --output option like this:

alapy_arc -c your_file.fastq.gz -o ~/alapy-archive/
alapy_arc -c your_file.fastq.gz --outdir ~/alapy-archive/
alapy_arc --compress your_file.fastq -o ~/alapy-archive/
alapy_arc --decompress your_file.ac --outdir ~/alapy-archive/

This will create output file in the specified directory called alapy-archive in your home directory.

Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each file is created in the same directory as the file which was processed. If output file already exists in place the name of the output file will be changed by adding the output file version.
You can rename the output file using -n or --name option like this:

alapy_arc -c your_file.fastq -n renamed_file
alapy_arc --compress your_file.ac --name renamed_file

This will create file called renamed_file.ac in the specified directory if -o or --outdir option is used or in the same directory as the input file. If file with the same name and location already exists, than the output file will be renamed be adding file version to it.
To suppress all progress messages on stdout and only report errors you can use option -q or --quiet like so:

alapy_arc -c your_file.fastq.gz -q
alapy_arc --decompress your_file.ac --quiet

As a result you will not see the progress in the output, but only error messages.
You may use multiple options in the same command, for example:

alapy_arc -c your_file.fastq -o ~/alapy-archive -q -n archived_file
These parameters will be interpreted by the ALAPY Compressor independently. Please refer to each command's help on this page.

WINDOWS BASIC COMMANDS AND USAGE EXAMPLES

To compress your fastq or fastq.gz file to ALAPY Compression format .ac file use option -c or --compress like so:

alapy_arc -c your.fastq
alapy_arc -c your.fastq.gz
alapy_arc --compress your.fastq
alapy_arc --compress your.fastq.gz

This will create your_file.ac file in the same directory as your original file unless you used option to change output directory (-o --outdir) or to change output file name (-n --name).

If you already have a file with output file name in place than version extension will be added
To decompress a .ac file of ALAPY Compression format to .fastq file use option -d or --decompress like so:

alapy_arc -d your_file.ac
alapy_arc --decompress your_file.ac

This will decompress the file in the same directory into your_filefastq.gz file unless you used option to change output directory (-o --outdir) or to change output file name (-n --name).

If you already have a file with output file name in place than version extension will be added
Create all output files in the specified output directory using -o --output option like this:

alapy_arc -c your_file.fastq.gz -o ~/alapy-archive/
alapy_arc -c your_file.fastq.gz --outdir ~/alapy-archive/
alapy_arc --compress your_file.fastq -o ~/alapy-archive/
alapy_arc --decompress your_file.ac --outdir ~/alapy-archive/

This will create output file in the specified directory called alapy-archive in your home directory.

Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each file is created in the same directory as the file which was processed. If output file already exists in place the name of the output file will be changed by adding the output file version.
You can rename the output file using -n or --name option like this:

alapy_arc -c your_file.fastq -n renamed_file
alapy_arc --compress your_file.ac --name renamed_file

This will create file called renamed_file.ac in the specified directory if -o or --outdir option is used or in the same directory as the input file. If file with the same name and location already exists, than the output file will be renamed be adding file version to it.
To suppress all progress messages on stdout and only report errors you can use option -q or --quiet like so:

alapy_arc -c your_file.fastq.gz -q
alapy_arc --decompress your_file.ac --quiet

As a result you will not see the progress in the output, but only error messages.
You may use multiple options in the same command, for example:

alapy_arc -c your_file.fastq -o ~/alapy-archive -q -n archived_file
These parameters will be interpreted by the ALAPY Compressor independently. Please refer to each command's help on this page.

GENERAL QUESTIONS

Yes! The current version of ALAPY Compressor and all future bugfixes are free forever. Lifetime support via email is also included. Enjoy!
No! You will not lose any data. We restore exact original fastq file you had bid by bid with the same md5 sum. Unfortunately there is no way to restore exact way your fastq file was compressed by gzip so fastq.gz files will differ in most cases. We are working on the algorithm that changes some of the information inside of fastq file but you will have access to completely lossless compression forever.
Magic, our love of data science and information entropy theory help us =) Also we like hard challenges!
You can write wrapper scripts, say on Unix using bash or other language of your choice. Or we can work together with you on this.
Most likely, yes. We are working on it right now.
Maybe we will make a free or payed GUI version in the future. We do not know if it is really needed. Could you please let us know by writing to compressor@alapy.com ?
We are working on efficient compression on alignment files (BAM, CRAM, etc) and have our own internal database for vcf storage and fast access. Please let us know how urgently and what exactly you need by write to compressor@alapy.com
You can write wrapper scripts, say on Unix using bash or other language of your choice. Or we can work together with you on this. By using our algorithm directly on multiple files compression levels can be improved compared to compressing multiple files separately. Also we are considering to add this functionality in the future. Not sure yet if this is going to be free or a little extra.
Yes at least for a few years while we support the current version. We might stop supporting it in the long term future, but the old versions will be available for much longer period until nobody needs it really.

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