Functions are live!
We're very happy to announce that the functionalities and tools we have developed are now live on both the Bioplatforms Data Portal and Galaxy Australia.
When you visit the Australian Microbiome "Processed Data" Search Page at the Data Portal you'll see a few new functions available in addition to improvements we've made to the contextual data search:
BLAST search - select an amplicon and enter any DNA sequence and a sequence similarity search will be undertaken against all data in the Australian Microbiome dataset. Results are downloadable in tabular format with sequence similarity scores, samples that include the matching sequence and geographical location (lat/lng) values of those samples:
Export Data To Galaxy Australia for further analysis - click on this and the data you have selected will be automatically sent to Galaxy Australia where there are 500+ analysis tools. We have wrapped tools for BIOM filtering and Ordination plotting (DCA, CCA, RDA, DPCoA, NMDS, MDS, PCoA), made these available to the global community, and installed these on Galaxy Australia. Both tools are based on R-scripts from the Phyloseq package:
Make Krona Taxonomic Abundance Graph using Galaxy Australia - click on this and the data you have selected will be automatically sent to Galaxy Australia and a workflow invoked to produce an interactive Krona graph. This can sometimes take a while to build if you've selected a large dataset but you'll be sent an email when the job is finished to view the outputs:
Export Search Results (BIOM) - if you do this and save the file to your computer, you can then upload the BIOM file straight into Phinch.org which is a sophisticated system for exploring taxonomic diversity and abundance:
You also don't have to be a user of the Bioplatforms Data Portal to use these tools and workflows.
Simply register for an account on Galaxy Australia and bring your own BIOM1 format files and you'll find the tools filed under 'Metagenomics' and the 'Visualise BIOM1 in Krona' workflow under the Shared Data > Workflows menu item:
____________________________________
When you visit the Australian Microbiome "Processed Data" Search Page at the Data Portal you'll see a few new functions available in addition to improvements we've made to the contextual data search:
BLAST search - select an amplicon and enter any DNA sequence and a sequence similarity search will be undertaken against all data in the Australian Microbiome dataset. Results are downloadable in tabular format with sequence similarity scores, samples that include the matching sequence and geographical location (lat/lng) values of those samples:
Export Data To Galaxy Australia for further analysis - click on this and the data you have selected will be automatically sent to Galaxy Australia where there are 500+ analysis tools. We have wrapped tools for BIOM filtering and Ordination plotting (DCA, CCA, RDA, DPCoA, NMDS, MDS, PCoA), made these available to the global community, and installed these on Galaxy Australia. Both tools are based on R-scripts from the Phyloseq package:
Make Krona Taxonomic Abundance Graph using Galaxy Australia - click on this and the data you have selected will be automatically sent to Galaxy Australia and a workflow invoked to produce an interactive Krona graph. This can sometimes take a while to build if you've selected a large dataset but you'll be sent an email when the job is finished to view the outputs:
Export Search Results (BIOM) - if you do this and save the file to your computer, you can then upload the BIOM file straight into Phinch.org which is a sophisticated system for exploring taxonomic diversity and abundance:
____________________________________
You also don't have to be a user of the Bioplatforms Data Portal to use these tools and workflows.
Simply register for an account on Galaxy Australia and bring your own BIOM1 format files and you'll find the tools filed under 'Metagenomics' and the 'Visualise BIOM1 in Krona' workflow under the Shared Data > Workflows menu item:
Comments
Post a Comment