Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences.

ABSTRACT: Avoiding biases in next generation sequencing (NGS) library preparation is crucial for obtaining reliable sequencing data. Recently, a new library preparation method has been introduced which has eliminated the need for the ligation step. This method, termed SMART (switching mechanism at the 5' end of the RNA transcript), is based on template switching reverse transcription. To date, there has been no systematic analysis of the additional biases introduced by this method. We analysed the genomic distribution of sequenced reads prepared from genomic DNA using the SMART methodology and found a strong bias toward long (≥12bp) poly dA/dT containing genomic loci. This bias is unique to the SMART-based library preparation and does not appear when libraries are prepared with conventional ligation

SUBMITTER: Vardi O 

PROVIDER: S-EPMC5325289 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature