Fig. 1

Overview of the information flow in the software package COGNATE. The Perl script COGNATE requires two files per run as input (blue): a fasta file containing the assembled nucleotide sequences and a GFF3 file with the protein-coding gene annotation information. The input (blue) is used to analyze genomic and genic features (green) on the level of assembly, SCSs, transcripts, CDSs, exons, and introns. Each complex of analyzed features is evaluated individually and the analyzed parameters are condensed in a step-wise manner by calculating means and medians (red). As output (yellow), 21 files are generated, of which all except two are in TSV format (the exceptions are: 00, protein fasta; 20, bash commands). The output files are split according to the analyzed features and parameters. All data files (02–13) are ordered by the ID of the respective feature. BATCH files (14–20) contain one entry line per genome and thus data of multiple COGNATE runs to facilitate direct comparisons of genomes. CDS: CoDing Sequence; GFF: Generic Feature Format; SCS: Scaffold or Contig Sequence; TSV: Tab-Separated Values