I would like to align the contigs from the recent  assembly of NA12878 to the latest human genome reference sequence (hg19). I have considered using BWA-SW, BLAT and LASTZ. I would greatly prefer to use the SAM/BAM format because it will facilitate my downstream analysis. However, BWA-SW prefers query sequences in the 1-2Mb range, while this assembly has contigs in the tens of megabases. LASTZ, on the other hand, is not well-suited for aligning to many chromosomes at once. BLAT is difficult because the PSL to BAM conversion is imperfect.
Has anyone done this?
If you were to do this, what tool would you use or how would you go about it?
 Gnerre et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA (2011) vol. 108 (4) pp. 1513-8