Because the default TMAP aligner [46] cannot align to references with more than 4.3 billion bases, it was necessary to use the BWA-SW aligner [47] to realign the Ion data to the diploid NA12878 reference for the error-rate comparison presented in Table S2 in Additional file 3, Figure S1 in Additional file 4, and Figure S2 in Additional file 5. To ensure that the comparison was only affected by the choice of reference, we also used BWA-SW to realign the Ion data to Human assembly 19 (GRCh 37) for those comparisons. The alignment was done using version 0.6.2 of the aligner with default parameters and the '-M' option to generate only one primary alignment per read (the analysis ignores secondary alignments).
