Background

Recently, several bio-projects dealing with the release of fungal genomes have transpired. Most of these projects use the new generation sequencing platforms. As a consequence, many de novo assembly tools have been devolved to assemble the reads generated by these platforms. Each tool has its own inherent advantages and disadvantages, which make the selection of appropriate tool a challenging problem.

Results

We have evaluated the performance of frequently used de novo assemblers namely ABySS, IDBA-UD, Minia, SOAP, SPAdes, Sparse, and Velvet. These assemblers are assessed based on their output quality during the assembly process conducted over fungal data.  We compared the performance of these assemblers by considering both computational as well as quality metrics. By analyzing these performance metrics, the assemblers are ranked and a tentative procedure for choosing the candidate assembler is illustrated.

Conclusions

In this study, we propose an assessment method for the selection of de novo assemblers by considering their computational as well as quality metrics at the draft genome level. We divide the quality metrics into three groups: g1 measures the goodness of the assemblies, g2 measures the problems of assemblies, and g3 measures the conservation elements in the assemblies. Our results demonstrate that the assemblers ABySS and IDBA-UD exhibit a good performance for the studied data from fungal genomes in terms of running time, memory, and quality. The results suggest that whole genome shotgun sequencing projects should make use of different assemblers by considering their merits. Our results are available for free for academic research at http://confluence.qu.edu.qa/display/download/bioinf