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.
Steven Stones-Havas - Geneious: Biocode and LIMS
- 1. Managing the Lab Workflow LIMS Software for Barcoding
- 2. Biocode LIMS Plugin Links to your existing field database EXCEL sheets, MySQL, Google Fusion Tables, and TAPIR Tracks your entire lab workflow All Extractions, PCR, and Sequencing reactions Produces reports on performance, finds errors Makes analysis easy Automated and visual sequence assembly pipeline Automatically generate sequence submissions (e.g. to Genbank)
- 3. Built on the power of Geneious
- 4. Built on the power of Geneious E-mail like interface Standard bioinformatics tools Consistent Windows, Mac, and Linux
- 5. Built on the power of Geneious Sequence and structure alignment Primer design and restriction analysis Phylogenetic and taxonomic tree building Contig assembly Publication searching Automatic search agents Collaboration
- 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
- 13. Binning Automatic categorization of reads and assemblies
- 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)
- 19. Verify Taxonomy BLASTs your sequences Gets the NCBI taxonomy for the best hit(s) Compares to the taxonomy from the FIMS
- 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
- 21. Thankyou LIMS plugin available on your conference USB sticks. http://software.mooreabiocode.org LIMS Walkthrough/demo – Wednesday 1pm-2pm, room LG29 Napier LIMS Clinic 1 – Friday 1pm-2pm, room 205 Napier LIMS Clinic 2 – Saturday 1pm-2pm, room 205 Napier
Editor's Notes
- #13: 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)
- #14: 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
- #15: *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
- #17: 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.
- #18: 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)
- #19: 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)