Jul 11, 2013

Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes

PloS One
Timothy T PerkinsB J Marshall

Abstract

The fully annotated genome sequence of the European strain, 26695 was first published in 1997 and, in 1999, it was directly compared to the USA isolate J99, promoting two standard laboratory isolates for Helicobacter pylori (H. pylori) research. With the genomic scaffolds available from these important genomes and the advent of benchtop high-throughput sequencing technology, a bacterial genome can now be sequenced within a few days. We sequenced and analysed strains J99 and 26695 using the benchtop-sequencing machines Ion Torrent PGM and the Illumina MiSeq Nextera and Nextera XT methodologies. Using publically available algorithms, we analysed the raw data and interrogated both genomes by mapping the data and by de novo assembly. We compared the accuracy of the coding sequence assemblies to the originally published sequences. With the Ion Torrent PGM, we found an inherently high-error rate in the raw sequence data. Using the Illumina MiSeq, we found significantly more non-covered nucleotides when using the less expensive Illumina Nextera XT compared with the Illumina Nextera library creation method. We found the most accurate de novo assemblies using the Nextera technology, however, extracting an accurate multi-locus sequence t...Continue Reading

  • References24
  • Citations14

References

  • References24
  • Citations14

Citations

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Peptic Ulcer
Genome
Tract
Helicobacter pylori
Ncbi Taxonomy
DNA Library
4,4',5'-trimethylazapsoralen
Gene Amplification Technique
Stomach Neoplasms

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