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(→Completing microbial genome assemblies: strategy and performance comparisons)
(→Completing bacterial genome assemblies: strategy and performance comparisons)
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  We therefore provide a comprehensive comparison by collecting datasets for the comparative assessment. In addition to offering explicit and useful recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly.    We therefore provide a comprehensive comparison by collecting datasets for the comparative assessment. In addition to offering explicit and useful recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly. 
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  Following a special methodology proposed by ALLPATHS-LG, the algorithm is supplied with three pre-prepared libraries—fragment, jump and long reads. ALLPATHS-LG is subsequently able to complete bacterial genomes as the sequencing coverage of fragment library is controlled at 100X. Although other hybrid approaches (including PacBio corrected reads pipeline, SPAdes, SSPACE-LongRead) could greatly improve continuity over the assembly produced by second-generation sequencing reads, we have demonstrated that such a hybrid approach is not efficient way to complete bacterial genomes. Both non-hybrid approaches—hierarchical genome-assembly process and PacBio corrected reads pipeline via self-correction—are able to produce complete genomes provided that the third generation sequencing reads are adequately long and complete.    Following a special methodology proposed by ALLPATHS-LG, the algorithm is supplied with three pre-prepared libraries—fragment, jump and long reads. ALLPATHS-LG is subsequently able to complete bacterial genomes as the sequencing coverage of fragment library is controlled at 100X. Although other hybrid approaches (including PacBio corrected reads pipeline, SPAdes, SSPACE-LongRead) could greatly improve continuity over the assembly produced by second-generation sequencing reads, we have demonstrated that such a hybrid approach is not efficient way to complete bacterial genomes. Both non-hybrid approaches—hierarchical genome-assembly process and PacBio corrected reads pipeline via self-correction—are able to produce complete genomes provided that the third generation sequencing reads are adequately long and complete. 
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