AUTHOR=Trivedi Urmi H. , Cézard Timothée , Bridgett Stephen , Montazam Anna , Nichols Jenna , Blaxter Mark , Gharbi Karim TITLE=Quality control of next-generation sequencing data without a reference JOURNAL=Frontiers in Genetics VOLUME=5 YEAR=2014 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2014.00111 DOI=10.3389/fgene.2014.00111 ISSN=1664-8021 ABSTRACT=

Next-generation sequencing (NGS) technologies have dramatically expanded the breadth of genomics. Genome-scale data, once restricted to a small number of biomedical model organisms, can now be generated for virtually any species at remarkable speed and low cost. Yet non-model organisms often lack a suitable reference to map sequence reads against, making alignment-based quality control (QC) of NGS data more challenging than cases where a well-assembled genome is already available. Here we show that by generating a rapid, non-optimized draft assembly of raw reads, it is possible to obtain reliable and informative QC metrics, thus removing the need for a high quality reference. We use benchmark datasets generated from control samples across a range of genome sizes to illustrate that QC inferences made using draft assemblies are broadly equivalent to those made using a well-established reference, and describe QC tools routinely used in our production facility to assess the quality of NGS data from non-model organisms.