After sequencing, reads were mapped to each genome reference sequence using the manufacturers’ alignment tools, tmap for PGM and blasr for PacBio (http://www.pacificbiosciences.com/products/software/algorithms). BWA [30 (link)] was used for mapping reads from the Illumina GAIIx, MiSeq and HiSeq. SAMtools [31 (link)] was then used to generate pileup and coverage information from the mapping output.
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