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. 2014;15 Suppl 9(Suppl 9):S10.
doi: 10.1186/1471-2164-15-S9-S10. Epub 2014 Dec 8.

Assessment of de novo assemblers for draft genomes: a case study with fungal genomes

Mostafa M Abbas, Qutaibah M Malluhi, Ponnuraman Balakrishnan

Assessment of de novo assemblers for draft genomes: a case study with fungal genomes

Mostafa M Abbas et al. BMC Genomics. 2014.

Abstract

Background: Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evolved to assemble the reads generated by these platforms. Each tool has its own inherent advantages and disadvantages, which make the selection of an appropriate tool a challenging task.

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 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 the 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.

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Figures

Figure 1
Figure 1
Comparison for N50 size metric for the studied assemblers at contigs level. (a): BcDw1, (b): UCRNP2, (c): UCRPA7, (d): UCREL1, (e): PST21.
Figure 2
Figure 2
Percentage of CEGs in four conservation groups for all assemblies at contigs level. CEGs Mapping results of the seven assemblers outputs and the current draft genome(df_1) at contigs level for the studied datasets in the four groups of core genes. (a): BcDw1, (b): UCRNP2, (c): UCRPA7, (d): UCREL1, (e): PST21.
Figure 3
Figure 3
Percentage of CEGs in four conservation groups for all assemblies at the scaffolds level. CEGs Mapping results of all assemblers outputs (except Minia) and the current draft genome(df_1) at scaffolds level for the studied datasets in the four groups of core genes. (a): BcDw1, (b): UCRNP2, (c): UCRPA7, (d): UCREL1, (e): PST21. In PST21 dataset, the df_1 represents the assemblies at the contigs level because we do not have scaffolds level.
See this image and copyright information in PMC

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