VODKA and VODKA2 workflows. (A) Brief description of the VODKA workflow starting with the DB generation from the last 3 kb of the reference genome to the generation of the report. (B) Preprocessing steps of RNA-sequencing reads to obtain nonhost reads. (C) VODKA2 catalog generation from a full-length reference genome. (D) Brief description of the VODKA2 analysis steps. Dashed arrows represent flow of information coming from the independent process of the VODKA2 analysis. Loop arrows show steps that run in parallel with LSF. (E) Content of the tabulated report. Information under the gray header is generated by both versions of the pipeline. The pink headers show additional information in the new VODKA2 version.
