Steven Stones-Havas - Geneious: Biocode and LIMS


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A basic introduction to the features of the LIMS plugin

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Steven Stones-Havas - Geneious: Biocode and LIMS

  1. 1. Managing the Lab Workflow <ul><li>LIMS Software for Barcoding </li></ul>
  2. 2. Biocode LIMS Plugin <ul><li>Links to your existing field database </li></ul><ul><ul><li>EXCEL sheets, MySQL, Google Fusion Tables, and TAPIR </li></ul></ul><ul><li>Tracks your entire lab workflow </li></ul><ul><ul><li>All Extractions, PCR, and Sequencing reactions </li></ul></ul><ul><ul><li>Produces reports on performance, finds errors </li></ul></ul><ul><li>Makes analysis easy </li></ul><ul><ul><li>Automated and visual sequence assembly pipeline </li></ul></ul><ul><ul><li>Automatically generate sequence submissions (e.g. to Genbank) </li></ul></ul>
  3. 3. Built on the power of Geneious
  4. 4. Built on the power of Geneious <ul><li>E-mail like interface </li></ul><ul><li>Standard bioinformatics tools </li></ul><ul><li>Consistent </li></ul><ul><li>Windows, Mac, and Linux </li></ul>
  5. 5. Built on the power of Geneious <ul><li>Sequence and structure alignment </li></ul><ul><li>Primer design and restriction analysis </li></ul><ul><li>Phylogenetic and taxonomic tree building </li></ul><ul><li>Contig assembly </li></ul><ul><li>Publication searching </li></ul><ul><li>Automatic search agents </li></ul><ul><li>Collaboration </li></ul>
  6. 6. Entering Data
  7. 7. Entering Data
  8. 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.
  9. 9. Tracking <ul><li>Workflows </li></ul>
  10. 10. Tracking <ul><li>Workflows </li></ul>
  11. 11. Tracking <ul><li>Graphical Reports </li></ul>
  12. 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. 13. Binning <ul><li>Automatic categorization of reads and assemblies </li></ul>
  14. 14. Trimming
  15. 15. Assembly Assembly – assembles the reads by name. You can also trim at this point if you didn’t do it before.
  16. 16. Assembly Report Assembly Binning Statistics
  17. 17. Alignment You can automatically align the consensus sequences from your assemblies (a common way to identify sequencing errors).
  18. 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. 19. Verify Taxonomy <ul><li>BLASTs your sequences </li></ul><ul><li>Gets the NCBI taxonomy for the best hit(s) </li></ul><ul><li>Compares to the taxonomy from the FIMS </li></ul>
  20. 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. 21. Thankyou <ul><li>LIMS plugin available on your conference USB sticks. </li></ul><ul><li> </li></ul><ul><li>LIMS Walkthrough/demo – Wednesday 1pm-2pm, room LG29 Napier </li></ul><ul><li>LIMS Clinic 1 – Friday 1pm-2pm, room 205 Napier </li></ul><ul><li>LIMS Clinic 2 – Saturday 1pm-2pm, room 205 Napier </li></ul>