Flow diagram for analysis of high-throughput sequencing data

Tex code and resulting pdf image, summarising the data processing pipeline of high-throughput sequencing data (fastq format files), through mapping the data to a reference genome, and then discovery and genotyping of sequence variants. The latter stage uses both 'GATK Haplotype Caller' for smaller variants, such as single-nucleotide polymorphisms and insertion-deletion polymorphisms, and Genomestrip for variants such as deletions and duplications greater than 1000 nucelotide bases in length. Note that the flow diagram is intended to represent what steps were take in the study, and does not necessarily represent the current optimum methods. The manuscript for which this image is a part of can be found open-access at F1000 Research "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" https://f1000research.com/articles/5-2644/v1 doi: 10.12688/f1000research.9912.