Quality control of next-generation sequencing data without a reference.
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.
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Urmi H
UH
Trivedi
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Timothée
T
Cézard
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Stephen
S
Bridgett
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Anna
A
Montazam
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Jenna
J
Nichols
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK ; Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Mark
M
Blaxter
Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh Edinburgh, UK ; Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK.
Karim
K
Gharbi
Illumina sequencing; PCR duplicates; de novo assembly; insert size; mate pair; quality control