We used GemSIM to calculate error models for and simulate reads from three different sequencing runs: Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry (Illumina v4); Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA (Illumina v5); and Roche/454 FLX Titanium (Roche/454). For the Illumina simulations, error models were calculated from PhiX control lane data aligned with Novocraft V2.07.06 [17]. Soft-clipping was disabled, reads aligning equally well to two genomic positions were randomly aligned to one of them, and the insert size was set with a standard deviation of 200. All other parameters were given their default values. 94.7% (v4) and 97.5% (v5) of reads aligned. For the Roche/454 simulation, we used aligned plasmid control data from a Hepatitis C Virus study [18]. This alignment was performed using Mosaik V1.1.0021 [19]. The maximum percentage mismatch allowed was increased to 1%, while all other parameters were set as recommended for Roche/454 Titanium. 85.4% of these reads aligned. Simulated reads were drawn from a set of B. aphidicola haplotypes, created by GemHaps using the B. aphidicola Cc reference genome [GenBank
