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In this article, we provide a comprehensive review of the above-motioned methods, and collect datasets for comparative assessment of the non-hybrid approaches—hierarchical genome-assembly process (HGAP) and self-correction approach (SCA). <u>In addition to offering explicit and useful recommendations to practitioners, the review guides to design a project in finishing microbial genome assembly.</u> Following a special recipe proposed by ALLPATHS-LG, to supply it with the three prepared libraries—fragment, jump and long reads, ALLPATHS-LG is able to complete microbial genomes as the sequencing coverage is controlled at 100X. Although the hybrid approach could improve the continuity over the assembly produced by the next-generation sequencing reads along, we did not successfully assemble a complete genome. The both non-hybrid approaches—HGAP and SCA—are able to produce complete genomes as long as the third generation sequencing reads are adequately long and sufficient. |
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In this article, we provide a comprehensive review of the above-motioned methods, and collect datasets for comparative assessment of the non-hybrid approaches—hierarchical genome-assembly process (HGAP) and self-correction approach (SCA). <u>In addition to offering explicit and useful recommendations to practitioners, the review guides to design a project in finishing microbial genome assembly.</u> Following a special recipe proposed by ALLPATHS-LG, to supply it with the three prepared libraries—fragment, jump and long reads, ALLPATHS-LG is able to complete microbial genomes as the sequencing coverage is controlled at 100X. Although the hybrid approach could improve the continuity over the assembly produced by the next-generation sequencing reads along, we did not successfully assemble a complete genome. The both non-hybrid approaches—HGAP and SCA—are able to produce complete genomes as long as the third generation sequencing reads are adequately long and sufficient. |
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= Datasets employed in this study =
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| align="center" style="background:#f0f0f0;"|'''Data'''
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| align="center" style="background:#f0f0f0;"|'''Organism'''
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| align="center" style="background:#f0f0f0;"|'''Fragment'''
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| align="center" style="background:#f0f0f0;"|'''Jump'''
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| align="center" style="background:#f0f0f0;"|'''Long read'''
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| align="center" style="background:#f0f0f0;"|'''Reference'''
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| D1||E. coli K-12 MG1655||2×101 bp, 180 bp insert (SRR447685)||2×93 bp, 3000 bp insert (SRR401827 and SRR492488)||1-3 Kbp (Ribeiro's ftpa)||NC_000913
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| D2||R. sphaeroides 2.4.1||2×101 bp, 180 bp insert (SRR125492)||2×101 bp, 3000 bp insert (SRR388672)||1-3Kbp (Ribeiro's ftpa)||NC_007488-90NC_007493-94NC_009007-08
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| D3||S. pneumoniae Tigr4||2×101 bp, 180 bp insert (SRR387335)||2×93 bp, 3000 bp insert (SRR364158)||1-3 Kbp (Ribeiro's ftpa)||NC_003028
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| D4||E. coli K-12 MG1655||2×151 bp, 300 bp insert (Illumina data websiteb)||||||NC_000913
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| D5||E. coli K-12 MG1655||||||10 Kbp, 17 SMRT cell (SRX255228c)||NC_000913
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| D6||E. coli K-12 MG1655||||||8-10 Kbp, 8 SMRT cells (SRX260475d)||NC_000913
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| D7||M. ruber DSM1279||||||8-10 Kbp, 4 SMRT cells (SRX260496d)||NC_013946
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| D8||P. heparinus DSM2366||||||8-10 Kbp, 7 SMRT cells (SRX260506d)||NC_013061
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| D9||E. coli K-12||||||PacBio RS II System and P4-C2 chemistrye, 20 Kbp library, 1 SMRT cell||NC_000913
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