====== CRUK-CI Genomics Indexes ======

Here are all the indexes in the Clarity LIMS system. Indexes are also known as "barcodes" and "reagent labels".

===== Special Cases =====

==== No Indexing ====

If your samples genuinely have no barcoding on them, and there should not be any index reads, use these values:

^ Index Type: | ''None''     |
^ Index:      | ''No Index'' |

It is very rare today that there is no indexing information to give a whole lane for one sample. If you're thinking of using this, best confirm with Genomics first.

==== Inline Barcodes ====

There are some techniques where the multiplexing index bases are not to be found in a separate read during sequencing, but are part of the actual sequencing read. If this is how you have done your barcoding, use these values:

^ Index Type: | ''In-Line Barcodes'' |
^ Index:      | ''INLINE''           |

The sequencing service will supply one or two FASTQ files per lane if this technique is used. Demultiplexing is down to the submitter.

==== Custom Indexing ====

New multiplexing kits appear all the time, and our system does not support every possible kit. If you are trying out a new kit, or the kit is not in the lists below, use this option.

^ Index Type: | ''Unspecified (Other)'' |
^ Index:      | ''Unspecified Index''   |

You will need to enter the number of cycles for your indexes in the SLX submission form in the ''Index Lengths'' field. If, for example, your kit is 8bp single index, enter "8" in the field. If your kit is 6bp and 10bp dual index, enter "6+10". Don't enter "n+0" (plus zero) for single index.\\
In this case, demultiplexing needs to be done by the user.

If your needs for indexing are not met by a supported kit, have a word with Genomics before confirming your submission. Experimental indexing will always need to be done as custom, but if you're using a new kit that is likely to go into general use we might add it to Clarity LIMS.

===== Supported Kits =====

{{scrape>https://genomicsequencing.cruk.cam.ac.uk/sequencing/help/IndexInformation!supported.action}}

===== Supported Index Type Mixes =====

There are some very specific cases where index types can be mixed (i.e. barcodes from more than one kit can be combined in a pool). **This is not recommended for general use** and should only be utilised under guidance from the Genomics Core.

{{scrape>https://genomicsequencing.cruk.cam.ac.uk/sequencing/help/IndexInformation!mixes.action}}

===== Barcoding Kit Details =====

{{scrape>https://genomicsequencing.cruk.cam.ac.uk/sequencing/help/IndexInformation!kits.action}}