Phylo_Forge_Script is a web application allowing to analyse fastq amplicon sequences of the 16S rRNA gene using the DADA2 analytical pipeline developed by Dr. Benjamin CALLAHAN. The application will provide an R object, which can then be analyzed using our script on your local computer or server. The script will provide a phyloseq object along with the ability to export all associated parameters used for it's creation. The phyloseq object can be further analyzed in our in house developed PhyloIgSeq application. Of note, Phylo_Forge is made to provide an analysis of 16S rRNA gene sequencing data along with a report that enables reproducing the analysis. In this respect we have aimed to follow the FAIR principles to facilitate downstream publication.
The Phylo_Forge application requires an excel file including two excel sheets: 1) FASTQs and 2) Metadata (in that order). (download example)
The FASTQs sheet should have the following columns (and no other): "Sample_ID", "Strand_nature", "File_name", "File_path".
The Metadata sheet should have the following columns (more can be added depending on the metadata to be included in the final ps object): "Sample_ID"
The Phylo_Forge_Script app creates an R object with all the parameters required to run the full DADA2 analysis of a 16S rRNA gene sequencing dataset. The analysis however should be run on a local server using a dedicated script (download here), which will create a full report including input data, parameters and analytical results as well as the final phyloseq object for downstream analysis.
Phylo_Forge_Script (full screen version)
Application authors: Julia ADELLE & Martin LARSEN
Application presentation by Julia ADELLE:
Web server administrator: Paul CASSAN