Creating Custom Sample Sheets
BaseSpace Clarity LIMS can create Illumina-based MiSeq and HiSeq 'flavoured' sample sheets. However, if you are using algorithms or indexes outside of those suggested by Illumina, you may be required to produce your own 'custom' sample sheet.
This example script provides an algorithm that harvests the contents of a flow cell (or any container) that may contain pooled samples, and uses the resulting information to output a custom sample sheet.
Solution
The attached script uses aggressive caching in order to execute as quickly as possible. When extreme levels of multiplexing are involved, the cache size could consume considerable quantities of memory, which may be counter-productive.
The algorithm has been tested on the following unpooled analytes; pooled analytes; and 'pools of pools' — in which multiple homogeneous or heterogeneous pools are themselves combined to produce a new pool
In these tests, the algorithm behaved as expected. If you find this is not the case please contact us.
| 1. | The algorithm uses recursion to determine the individual analytes (samples) and their indexes that are located on the flow cell lane(s). |
| 2. | To determine whether an analyte constitutes a pool or not, the script looks at the number of submitted samples with which the analyte is associated. |
| • | If the answer is 1, the analyte is not a pool. |
| • | If the answer is greater than 1, the analyte is considered to be a pool. |
| 3. | If a pooled analyte is discovered, the inputs of the process that produced the pooled analyte are gathered and the same test is used to see if they themselves are pools. |
| 4. | This gathering of ancestor analytes continues until the contents of each pool have been resolved, at which point the script produces some example output. |
| • | Note that while it is expected that you will augment this section of the script with the fields you need for your custom sample sheet, the logic to recursively identify analytes that are not themselves pools should be applicable to all. |
Parameters
The script is invoked with just three parameters:
|
-l |
The luid of the flow cell / container of interest (Required) |
|
-u |
The username of the current user (Required) |
|
-p |
The password of the current user (Required) |
An example of the full syntax to invoke the script is as follows:
/usr/bin/python /opt/gls/clarity/customextensions/flowcellContents.py -l 27-1234 -u admin -p securepassword
Assumptions and Notes
| • | Both of the attached files are placed on the Clarity LIMS server, in the /opt/gls/clarity/customextensions folder. |
| • | You will need to implement your own logic to gather the fields required for your specific sample sheet. |
| • | You will need to update the HOSTNAME global variable such that it points to your Clarity LIMS server. |
| • | The example code is provided for illustrative purposes only. It does not contain sufficient exception handling for use 'as is' in a production environment. |
