The profile for regional GC content versus mean target coverage, produced by using the default settings for the relevant <i>ArtificialFastqGenerator</i> user parameters.

<p>The profile for regional GC content versus mean target coverage, produced by using the default settings for the relevant <i>ArtificialFastqGenerator</i> user parameters.</p

Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines

<div><p>Pipelines for the analysis of Next-Generation Sequencing (NGS) data are generally composed of a set of different publicly available software, configured together in order to map short reads of a genome and call variants. The fidelity of pipelines is variable. We have developed <em>ArtificialFastqGenerator</em>, which takes a reference genome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores. Since these artificial FASTQs are derived from the reference genome, it provides a gold-standard for read-alignment and variant-calling, thereby enabling the performance of any NGS pipeline to be evaluated. The user can customise DNA template/read length, the modelling of coverage based on GC content, whether to use real Phred base quality scores taken from existing FASTQ files, and whether to simulate sequencing errors. Detailed coverage and error summary statistics are outputted. Here we describe <em>ArtificialFastqGenerator</em> and illustrate its implementation in evaluating a typical bespoke NGS analysis pipeline under different experimental conditions. <em>ArtificialFastqGenerator</em> was released in January 2012. Source code, example files and binaries are freely available under the terms of the GNU General Public License v3.0. from <a href="https://sourceforge.net/projects/artfastqgen/">https://sourceforge.net/projects/artfastqgen/</a>.</p> </div

Regional association plot of the 1q24.1 risk locus.

<p>The figure shows −log₁₀<i>P</i> values (y-axis) versus chromosomal positions (x-axis; NCBI build 37). Genotyped SNPs are shown as triangles, with imputed SNPs as circles. rs3845536 has been highlighted through the use of a larger symbol. Colour intensity is proportional to LD with rs3845536: from white (<i>r</i>² = 0) to red (<i>r</i>² = 1.0). The light blue line indicates genetic recombination rates (estimated from 1000 Genomes Phase 1 CEU data). Nearby genes and transcripts are also shown.</p