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Welcome to the BWP Informatics Documentation!

This documentation site describes the best practices for the informatics pipeline of the Barcode of Wildlife Project.

Updates

11 September, 2017
Biocode plugin updated to fix problem where the Biocode FIMS only retrieved field definitions from the Barcode of Wildlife project instead of the project that was specified. This would result in empty tissue fields.
20 September, 2016
The GenBank submission plugin was updated to version 1.6.5 with many minor bug fixes. The most important one to the BWP project is that the plugin will now attemp to replace non-ASCII characters (such as accented characters) with equivalent ASCII characters. This has been a problem in the past, since the previous default action was to simply omit these characters.
15 June, 2016
The Biocode Plugin was updated to version 3.0.0, and the GenBank Upload Plugin was updated to version 1.6.4. You can read about the updates to the Biocode Plugin here. You can read about the updates to the GenBank Upload Plugin here. Additionally, the back-end LIMS database was split up by country and new login information was provided to each BWP partner via email.
.. toctree::
        :caption: Background

        workflow
        software_components
        barcode_data_standard
        bwp_data_standard
        conventions

.. toctree::
        :maxdepth: 2
        :caption: FIMS

        fims_spreadsheet_pop
        fims_spreadsheet_val

.. toctree::
        :maxdepth: 2
        :caption: LIMS

        geneious_intro
        biocode_plugin
        extraction_plates
        pcr_plates
        cyclesequencing_plates

.. toctree::
        :maxdepth: 2
        :caption: Sequence Assembly and Publication

        downloading_traces
        assembling_contigs
        sequence_qc
        mark_pass
        gb_upload
        its_annotation

.. toctree::
        :maxdepth: 2
        :caption: Troubleshooting

        lims_connection
        lims_migration