Implication of quality score for de novo transcriptome reconstruction of Illumina reads

Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly.

Using RNA-Seq data produced from Illumina, researchers at the University of the Western Cape, South Africa teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. They showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. These data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, these results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms.


Mbandi SK, Hesse U, Rees DJ, Christoffels A. (2014) A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads. Front Genet 5, 17. [article]