Special files to install for Illumina Experiment Manager

[Joe Foley]

Depending on your indexing scheme, you may need to install the attached files (Smart-3SEQ_IEM.zip) into your copy of Illumina Experiment Manager in order to generate sample sheets for demultiplexing Smart-3SEQ data.

• If you use only the 24 legacy single indexes without asterisks in the protocol (the standard set of Illumina's 24 "LT" indexes), you can simply use the built-in "TruSeq Single Indexes" option and you don't need to install these files.
  
• If you use the UDI index pairs (both i5 and i7), you can use the built-in "UD Indexes (96 Indexes)" option and you don't need to install these files.
• If you use the other 24 legacy single indexes with asterisks, you must install these files.
• If you use the unusual i5-only indexing scheme, you must install these files.

The default installation directory for IEM, where these files must go, is C:\Program Files (x86)\Illumina\Illumina Experiment Manager and you must have administrator privileges to add these files there. 

Warning: If you have previously installed other custom IEM files, this will overwrite your existing changes to Applications\NextSeqGenerateFASTQ.txt. Instead you can simply edit your existing file and add one new line for the "Smart-3SEQ" sample prep kit. If you are using a workflow other than "NextSeq FASTQ Only" you may need to add this line in the corresponding file instead.

Once this is added, you can set your "Library Prep Workflow" to "Smart-3SEQ" and then select the appropriate indexing scheme. PROTIP: You can copy and paste a column of index numbers (single-indexing) or plate wells (dual indexing) from another program (e.g. spreadsheet editor) into the "Sample Selection" interface, rather than click numerous times for each sample. The attached TSV file has lists of all the 96-plex plate wells sorted by row or by column. Also note the "Reagent Kit Barcode" does not have to correspond to anything and determines the name of the output file, so you can name it according to the experiment.

[Joe Foley]

The configuration files from the previous message are no longer compatible with IEM version 1.19. Updated files are attached to this message.

[Joe Foley]

These configuration files add support for i5-only indexing on the MiSeq and remove a few extraneous options to reduce confusion. If IEM is already working for you and you aren't using a MiSeq, you don't need this update. Otherwise, please uninstall IEM and delete the leftover installation folder (default C:\Program Files (x86)\Illumina\Illumina Experiment Manager) for good measure, then reinstall IEM 1.19.1 and copy these new files into that folder (requires administrator privileges). If you are using other custom IEM configuration files, you will have to merge the changes by hand.