Nucleic Acids Research Advance Access published online on July 26, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn425
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Methods Online |
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
1Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin and 2Institute for Functional Genomics, Computational Diagnostics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany
*To whom correspondence should be addressed. Tel: +49 30 8413 1354; Fax: +49 30 8413 1380; Email: himmelbauer{at}molgen.mpg.de
Received December 21, 2007. Revised June 16, 2008. Accepted June 19, 2008.
Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A > C transversion being among the most frequent and C > G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.