@article{TEXTUAL,
      recid = {10827},
      author = {Losada, Liliana and Varga, John J. and Hostetler, Jessica  and Radune, Diana and Kim, Maria and Durkin, Scott and  Schneewind, Olaf and Nierman, William C.},
      title = {Genome Sequencing and Analysis of &amp;lt;i&amp;gt;Yersina  pestis&amp;lt;/i&amp;gt; KIM D27, an Avirulent Strain Exempt from  Select Agent Regulation},
      journal = {PLOS ONE},
      address = {2011-04-29},
      number = {TEXTUAL},
      abstract = {&lt;p&gt;&lt;em&gt;Yersinia pestis&lt;/em&gt; is the causative agent of the  plague. &lt;em&gt;Y. pestis&lt;/em&gt; KIM 10+ strain was passaged and  selected for loss of the 102 kb &lt;em&gt;pgm&lt;/em&gt; locus,  resulting in an attenuated strain, KIM D27. In this study,  whole genome sequencing was performed on KIM D27 in order  to identify any additional differences. Initial assemblies  of 454 data were highly fragmented, and various  bioinformatic tools detected between 15 and 465 SNPs and  INDELs when comparing both strains, the vast majority  associated with A or T homopolymer sequences. Consequently,  Illumina sequencing was performed to improve the quality of  the assembly. Hybrid sequence assemblies were performed and  a total of 56 validated SNP/INDELs and 5 repeat differences  were identified in the D27 strain relative to published KIM  10+ sequence. However, further analysis showed that 55 of  these SNP/INDELs and 3 repeats were errors in the KIM 10+  reference sequence. We conclude that both 454 and Illumina  sequencing were required to obtain the most accurate and  rapid sequence results for &lt;em&gt;Y. pestis&lt;/em&gt; KIMD27. SNP  and INDELS calls were most accurate when both Newbler and  CLC Genomics Workbench were employed. For purposes of  obtaining high quality genome sequence differences between  strains, any identified differences should be verified in  both the new and reference genomes.&lt;/p&gt;},
      url = {http://knowledge.uchicago.edu/record/10827},
}