The murine malaria parasite Plasmodium berghei is a robust and safe malaria model organism. The N15 phage-derivative, low-copy pJAZZ® vector system (from Lucigen) can carry large, AT-rich inserts in a stable manner. We have exploited pJAZZ®, to successfully generate a large-insert P. berghei genomic library. Furthermore, we have established a scalable pipeline to effectively convert the genomic library into large-scale genetic modification vector libraries (Pfander et al. 2011). These vector libraries are the basis for PlasmoGEM (http://plasmogem.sanger.ac.uk/), an open-access genome-scale Plasmodium genetic modification resource, initially focused on P. berghei and hosted by WTSI. PlasmoGEM vectors benefit from a significantly increased transfection efficency due to their long homlogy arms, are equipped with unique moloecular barcodes and are genereatedin absence of error-prone PCR amplification. Crucial to the performance of these vectors upon transfection is their sequence integrity. To ensure only the gene of interets held on the large-insert genomic clone is modified in the intended manner, in absence of genetic artefacts such as unforseen insertions or deletions, we propose to use Illumina MiSeq for full-length sequencing as a part of our quality control of PlasmoGEM gene targeting vectors.