use cases
In this repo, we present a full example of the metaGOflow pipeline using actual EMO BON sequence data.
TARA OCEANS sample
Marine, surface layer water
- Study accession number: PRJEB1787
- Sample accession number: ERS490265
- Run accession number: ERR599171
Quality control
metaGOflow invokes fastp that automatically returns a .html report like the one below for the case of this water column sample:
Taxonomic inventory
metaGOflow uses the mapSEQ to extract taxa present on the community based on the ribosomal RNA sequences.
Here is the krona plot metaGOflow returns as a visual component of the community structure.
Functional annotation
metaGOflow supports a functional annotation step that uses the filtered reads and a series of tools and databases to return several types of annotations.
InterProScan (IPS)
On the first column we get the number of hits an id had among the reads, on the second the IPS id and on the third its description.
GO-slim
GO slim is a cut-down version of the GO ontologies that contain only a subset of terms from the GO resource. metaGOflow provides both a full GO annotation which is not displayed here as it is rather long and a slim version like the one shown here for the water column case. On the first column there is the GO id, on the second its description, on the third its the GO ontology it belogs to (biological process, cellular component, molecular function) and on the fourth one we have the number of hits of the annotation on the reads.
KEGG terms (KOs)
Similar to the IPS case, on the first column we get the number of hits an id had among the reads, on the second the KO and on the third its description.
Pfam
Like in the IPS and the KEGG cases.