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2017 ; 18
(1
): 93
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A comparative evaluation of genome assembly reconciliation tools
#MMPMID28521789
Alhakami H
; Mirebrahim H
; Lonardi S
Genome Biol
2017[May]; 18
(1
): 93
PMID28521789
show ga
BACKGROUND: The majority of eukaryotic genomes are unfinished due to the
algorithmic challenges of assembling them. A variety of assembly and scaffolding
tools are available, but it is not always obvious which tool or parameters to use
for a specific genome size and complexity. It is, therefore, common practice to
produce multiple assemblies using different assemblers and parameters, then
select the best one for public release. A more compelling approach would allow
one to merge multiple assemblies with the intent of producing a higher quality
consensus assembly, which is the objective of assembly reconciliation. RESULTS:
Several assembly reconciliation tools have been proposed in the literature, but
their strengths and weaknesses have never been compared on a common dataset. We
fill this need with this work, in which we report on an extensive comparative
evaluation of several tools. Specifically, we evaluate contiguity, correctness,
coverage, and the duplication ratio of the merged assembly compared to the
individual assemblies provided as input. CONCLUSIONS: None of the tools we tested
consistently improved the quality of the input GAGE and synthetic assemblies. Our
experiments show an increase in contiguity in the consensus assembly when the
original assemblies already have high quality. In terms of correctness, the
quality of the results depends on the specific tool, as well as on the quality
and the ranking of the input assemblies. In general, the number of misassemblies
ranges from being comparable to the best of the input assembly to being
comparable to the worst of the input assembly.
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