Workflows

This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

This workflow creates taxonomic summary tables for a specified taxonomic rank out of MAPseq's OTU tables output collection.

The MAPseq to Ampvis workflow processes MAPseq OTU tables and associated metadata for analysis in Ampvis2. This workflow involves reformatting MAPseq output datasets to produce structured output files suitable for Ampvis2.

MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.

Classification and visualization of ITS regions.

Quality control subworkflow for paired-end reads.

Quality control subworkflow for single-end reads.

Classification and visualization of SSU, LSU sequences.

This workflow creates taxonomic summary tables out of the amplicon pipeline results.