References Management Guide

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References Management Guide TOC

Upload a New Reference File

As part of the standard analysis process, reads are aligned to a genomic reference, using the TMAP aligner that comes pre-installed on the Torrent Server. The alignments and some summary statistics based on the alignments are included in the Run Report Metrics Before Alignment of the Torrent Browser Analysis Report Guide .

For a new genome sequence, use the Admin > References tab to add the new reference genome. (These reference sequences are also displayed on the Ion S5, Ion PGM, or Ion Proton Sequencer when you load a sample.)

Prerequistes

The following are prerequisites to uploading a new reference file:

• Create a FASTA format reference sequence file (on your client machine).
  
  
  
  

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  FASTA files can be found at: http://www.ncbi.nlm.nih.gov/sites/genome
  
  Download the FASTA file to your local client machine.

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  It is important that the format of your FASTA file conform to Ion Torrent requirements.

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  When working with larger genomes, performance improves if you first zip the FASTA file. The create index tool supports a zip archive, provided the file contains only a single FASTA file.

• Prepare a descriptive name for the genome.
• Prepare the short name for the genome.
• Prepare a version for the genome.
• Know the number of reads to randomly sample for alignment.
• Prepare a regions of interest file or hotspots file (on your client machine).

Upload the reference

You upload reference files with the Admin gear menu References tab:

Follow these steps to upload a reference genome:

1. On the Admin > References tab, in the References Sequences section, click the Upload a Custom Reference button:
   
   
   
   
   
   
   
   

2. Fill out the Add New Reference Genome page. Required fields are noted on the page.
   
   
   
   
   
   
   
   
   
   

   Field	Description
   Descriptive name	[required]This entry may be any text string. The description usually includes the genus-species, version, and other identifying information. The description entered here is displayed in various report output, and is listed in the Reference Sequences section of the Admin > References tab.
   Short name	[required] A shortened form of the genome name, the short form of the genome name may be any alphanumeric character and the underscore (_) character. The name should not match any existing references installed in the /results/referenceLibrary /<index_type>/<genome_shortname>/ directory, including previous unsuccessful attempts at creating reference sequences. Undesired sequences can be removed. Deletion allows the short name to be used for a new genome.
   Genome version	[required] Enter any string for the genome version number. The accession number, if there is one, is a good choice. The version entered here is displayed in various report outputs.
   Notes	[optional] Use this field to record any notes about the reference genome

3. Click the Select File button and browse to the genome file (on your local machine).
   
   
   
   
4. Click the Upload file and create reference button.
   
   
   
   
5. Wait while the genome is uploaded.
   
   
   
   

After the reference is created, you can optionally add target regions BED files and hotspots BED or VCF files to the reference. See Manage Target Regions Files and Hotspot Files .

Error Handling

If you uploaded an invalidly formatted FASTA file, the following error displays when you attempt to view the reference sequence associated with the file:







To recover from the error:

1. Delete the existing reference sequence entry.
2. Identify and correct formatting errors in the FASTA file.
3. Retry Upload the reference .

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