Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.

ABSTRACT:

Background

The generation and analysis of high-throughput sequencing data are becoming a major component of many studies in molecular biology and medical research. Illumina's Genome Analyzer (GA) and HiSeq instruments are currently the most widely used sequencing devices. Here, we comprehensively evaluate properties of genomic HiSeq and GAIIx data derived from two plant genomes and one virus, with read lengths of 95 to 150 bases.

Results

We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observ

SUBMITTER: Minoche AE 

PROVIDER: S-EPMC3334598 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature