Steven Stones-Havas - Geneious: Biocode and LIMS
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The document discusses a LIMS software plugin that can: 1) Link to existing field databases like Excel, MySQL, and Google Fusion Tables to track an entire lab workflow from extractions to sequencing. 2) Produce reports on performance and find errors to make analysis easy. 3) Automatically generate sequence submissions to databases like GenBank.
![Managing the Lab Workflow ,[object Object]](https://image.slidesharecdn.com/monday20-20napier2010220-20164020-20stone-havas20s20-20biocodelimsshortpresentation1-111129224520-phpapp01/85/Steven-Stones-Havas-Geneious-Biocode-and-LIMS-1-320.jpg)
![Biocode LIMS Plugin ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
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Steven Stones-Havas - Geneious: Biocode and LIMS
- 3. Built on the power of Geneious
- 8. Entering Data The checkboxes on the left tell Geneious whether to edit the fields. If checked, all selected reactions will have that field set to the entered value. If unchecked, the fields will be left as they are.
- 12. Data analysis Here are the traces. You can see some FIMS data in the document fields (eg identified by, tissue id). You will also notice a binning column
- 14. Trimming
- 15. Assembly Assembly – assembles the reads by name. You can also trim at this point if you didn’t do it before.
- 16. Assembly Report Assembly Binning Statistics
- 17. Alignment You can automatically align the consensus sequences from your assemblies (a common way to identify sequencing errors).
- 18. Tree We can check that like taxa are grouped together correctly by generating a tree (a good indication that the sequences we are getting back match the organisms we think we collected)
- 20. Submit to Genbank You can map fields from your FIMS and LIMS to Genbank fields for easy submission. Your barcodes are automatically validated and uploaded to NCBI
Editor's Notes
- Here are the traces. You can see some FIMS data in the document fields (eg identified by, tissue id). You will also notice a binning column (see the following slide)
- Binning is a huge timesaver –high binned reads are OK to pass onto the next step in the workflow, and low binned reads can be rejected for resequencing. This means that only ~10% of the data needs to be examined by the scientist
- *Let’s trim the reads to try and move them into higher bins. Run through the options quickly. Geneious annotates the trims, rather than just removing them like other programs. This means you don’t lose any data, and can re-trim later on if you want to redo your workflow
- When the process is finished, you get a bunch of pairwise assemblies, which are binned according to the binning parameters (center box). You also get an assembly report telling you exactly which reads were and were not assembled.
- I this case we are sequencing a coding region, so as an additional validation step we can color bases by their translaton to look for internal stop codons (they will show up in black)
- We can check that simlar taxa are grouped together in the tree (a good indication that the sequences we are getting back match the organisms we think we collected)