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- Title
Quality control of next-generation sequencing data without a reference.
- Authors
Trivedi, Urmi H.; Cézard, Timothée; Bridgett, Stephen; Montazam, Anna; Nichols, Jenna; Blaxter, Mark; Gharbi, Karim
- 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.
- Subjects
POLYMERASE chain reaction; NUCLEOTIDE sequencing; GENOMICS; GENOME size; QUALITY control
- Publication
Frontiers in Genetics, 2014, Vol 5, p1
- ISSN
1664-8021
- Publication type
Article
- DOI
10.3389/fgene.2014.00111