Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation
Fig 2
The structural workflow chains together tools in Galaxy for gene calling.
The structural workflow accepts as input a nucleotide FASTA genome sequence, and processes it through ARAGORN for tRNAs (dark noodles), Glimmer and MetaGeneAnnotator for high-confidence gene predictions (golden and teal, respectively), and Get ORFs as a naïve ORF/CDS caller (magenta). Potential protein-coding genes are filtered to ensure the presence of a phage (ATG/GTG or TTG) start codon and a Shine-Dalgarno feature is added to all features that have a detectable match. These are interconverted between formats and the gene models are corrected for display in Apollo.