steven stones-havas - geneious: biocode and lims
DESCRIPTION
A basic introduction to the features of the LIMS pluginTRANSCRIPT
Managing the Lab WorkflowManaging the Lab WorkflowLIMS Software for BarcodingLIMS Software for Barcoding
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)
Built on the power of Geneious
Built on the power of Geneious
• E-mail like interface
• Standard bioinformatics tools
• Consistent
• Windows, Mac, and Linux
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
Entering Data
Entering Data
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.
Tracking
• Workflows
Tracking
• Workflows
Tracking
• Graphical Reports
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
Binning• Automatic categorization of reads and
assemblies
Trimming
Assembly
Assembly – assembles the reads by name. You can also trim at this point if you didn’t do it before.
Assembly
ReportAssembly Binning
Statistics
Alignment
You can automatically align the consensus sequences from your assemblies (a common way to identify sequencing errors).
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)
Verify Taxonomy• BLASTs your sequences• Gets the NCBI taxonomy for the best hit(s)• Compares to the taxonomy from the FIMS
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
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