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(→Datasets employed in this study)
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(→Datasets employed in this study)
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| We have conducted a <span style="color:blue;">hybrid approach</span> proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (<span style="color:blue;">D5</span>) with short reads (<span style="color:blue;">D4</span>) (by [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA PacBioToCA]), then to ''de novo'' assemble the corrected long reads (by [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=runCA runCA]) for ''E. coli'' genome reconstruction. | We have conducted a <span style="color:blue;">hybrid approach</span> proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (<span style="color:blue;">D5</span>) with short reads (<span style="color:blue;">D4</span>) (by [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA PacBioToCA]), then to ''de novo'' assemble the corrected long reads (by [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=runCA runCA]) for ''E. coli'' genome reconstruction. | ||
| - | We have conducted the both non-hybrid approaches: <span style="background-color:#D4F2CE;">hierarchical genome-assembly process (HGAP)</span> and <span style="background-color:#D4F2CE;">self-correction approach (SCA)</span> to ''de novo'' assemble the PacBio long reads. The datasets used in the non-hybrid approach are composed of various SMRT cells, ranging from 4 to 17 XL-C2 SMRT cells (D5-D8), and a single SMRT cell gathered with PacBio RS II system and P4-C2 chemistry (D9). | + | We have conducted the both non-hybrid approaches: <span style="background-color:#D4F2CE;">hierarchical genome-assembly process (HGAP)</span> and <span style="background-color:#D4F2CE;">self-correction approach (SCA)</span> to ''de novo'' assemble the PacBio long reads. The datasets used in the non-hybrid approach are composed of various SMRT cells, ranging from 4 to 17 XL-C2 SMRT cells (<span style="background-color:#D4F2CE;">D5-D8</span>), and a single SMRT cell gathered with PacBio RS II system and P4-C2 chemistry (<span style="background-color:#D4F2CE;">D9</span>). |
| {| {{table}} border="1" | {| {{table}} border="1" | ||
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| - | | <span style="color:blue;">D5</span>||E. coli K-12 MG1655||||||10 Kbp, 17 SMRT cell (SRX255228<sup>c</sup>)||NC_000913 | + | | <span style="color:blue;background-color:#D4F2CE;">D5</span>||E. coli K-12 MG1655||||||10 Kbp, 17 SMRT cell (SRX255228<sup>c</sup>)||NC_000913 |
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| - | | D6||E. coli K-12 MG1655||||||8-10 Kbp, 8 SMRT cells (SRX260475<sup>d</sup>)||NC_000913 | + | | <span style="background-color:#D4F2CE;">D6</span>||E. coli K-12 MG1655||||||8-10 Kbp, 8 SMRT cells (SRX260475<sup>d</sup>)||NC_000913 |
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| - | | D7||M. ruber DSM1279||||||8-10 Kbp, 4 SMRT cells (SRX260496<sup>d</sup>)||NC_013946 | + | | <span style="background-color:#D4F2CE;">D7</span>||M. ruber DSM1279||||||8-10 Kbp, 4 SMRT cells (SRX260496<sup>d</sup>)||NC_013946 |
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| - | | D8||P. heparinus DSM2366||||||8-10 Kbp, 7 SMRT cells (SRX260506<sup>d</sup>)||NC_013061 | + | | <span style="background-color:#D4F2CE;">D8</span>||P. heparinus DSM2366||||||8-10 Kbp, 7 SMRT cells (SRX260506<sup>d</sup>)||NC_013061 |
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| - | | D9||E. coli K-12||||||PacBio RS II System and P4-C2 chemistry<sup>e</sup>, 20 Kbp library, 1 SMRT cell||NC_000913 | + | | <span style="background-color:#D4F2CE;">D9</span>||E. coli K-12||||||PacBio RS II System and P4-C2 chemistry<sup>e</sup>, 20 Kbp library, 1 SMRT cell||NC_000913 |
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| |} | |} | ||