If you are choosing between Illumina and Ion Torrent for sequencing of your genome of interest, a study published recently by the Broad Institute (Ross et al 2013 Genome Biology 14:R51) may be of interest to you.
The study compares Illumina MiSeq, Ion Torrent PGM and PacBio on sequencing bias in regions with extreme GS content (<10% and >75%) or long AT dinucleotides in three different bacterial genomes. Relative coverage by each technology is lower in all of these difficult regions, but coverage bias was found to be the most pronounced in Ion Torrent PGM data. PacBio demonstrates the least coverage bias, likely because of its amplication-free protocol, but a much higher error rate than the other two platforms was observed. The results are consistent with an earlier study that also compared those same sequencing platforms (Quail et al 2012 BMC Genomics. 13: 341).
Therefore, depending on the characteristics of your genome of interest, your choice of sequencing platform will influence your downstream analyses.