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Quality control of next-generation sequencing data without a reference

ABSTRACT: Quality control of next-generation sequencing data without a reference

PROVIDER: PRJEB5201 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR409719_1.fastq.gz	Fastqsanger.gz
	ERR409719_2.fastq.gz	Fastqsanger.gz
	ERR409720_1.fastq.gz	Fastqsanger.gz
	ERR409720_2.fastq.gz	Fastqsanger.gz
	ERR409721_1.fastq.gz	Fastqsanger.gz

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Quality control of next-generation sequencing data without a reference.

Project description: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.

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Project description:We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL webcite.

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