Genomic DNA was isolated from Vibrio cholerae strains N16961 and TRH7000 and six type II secretion system (T2SS) mutants of TRH7000 called delta-epsL, delta-epsG1, delta-epsG2, delta-epsM, PU3 and PU5 using Wizard Genomic DNA Purification kit from Promega. Paired-end libraries were constructed and sequencing was performed with a read-length of 100x100 by the University of Michigan DNA Sequencing Core using Illumina HiSeq 2000 to identify possible secondary mutations in the T2SS mutants.