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Rockhopper workflow. The input to Rockhopper consists of a genome sequence (FASTA file), gene annotations (PTT and RNT files) and sequencing reads (FASTQ or QSEQ or FASTA files). The different stages of Rockhopper’s workflow are illustrated. Rockhopper’s results are output as tab-delimited text files as well as visually using the Integrated Genomics Viewer.
