steven stones-havas - geneious: biocode and lims

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