Schematic representation of the customized pipeline for automated sequence processing. After demultiplexing using DDemux, quality scores of individually sorted raw sequencing reads are converted to Sanger format. Reads are then filtered and trimmed according to the given parameters. Retained reads are then synchronyzed as pairs with identical coordinates, and unpaired reads sorted as orphans. Paired reads are aligned to the reference genome using Bowtie . Unaligned and orphan reads are then joined, and user can choose to perform single read alignment. Finally, all aligned reads are joined and are ready for a variant calling pipeline.