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We have used ALLPATHS-LG to assemble three bacterial genomes: [[E. coli]], [[R. sphaeroides]], and [[S. pneumoniae]]. The sequencing reads for these three genome assemblies are summarized in the following table (D1-D3).

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We have conducted a hybrid approach proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (D5) with short reads (D4) (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 firstly investigated the effect of sequencing depths on assembly ([[Read Depths]]), then set genome size in running [[pacBioToCA]], finally we tried different specs for [[runCA]].

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We have conducted a hybrid approach proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (D5) with short reads (D4) (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 firstly investigated the effect of sequencing depths on assembly ([[Read Depths]]), then set genome size in running [[pacBioToCA]], finally we tried different Celera Assembler parameters for [[runCA]].

We have conducted the both non-hybrid approaches: hierarchical genome-assembly process ([[HGAP]]) and self-correction approach ([[SCA]]) 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 used <span style="color:#FF0000;background-color:#ffffcc;">ALLPATHS-LG</span> to assemble three bacterial genomes: [[E. coli]], [[R. sphaeroides]], and [[S. pneumoniae]]. The sequencing reads for these three genome assemblies are summarized in the following table (<span style="color:#FF0000;background-color:#ffffcc;">D1-D3</span>).
-								We have conducted a <span style="color:#0000FF;">hybrid approach</span> proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (<span style="color:#0000FF;">D5</span>) with short reads (<span style="color:#0000FF;">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 firstly investigated the effect of sequencing depths on assembly ([[Read Depths]]), then set genome size in running [[pacBioToCA]], finally we tried different specs for [[runCA]].
+								We have conducted a <span style="color:#0000FF;">hybrid approach</span> proposed by Koren ''et al.''([http://www.ncbi.nlm.nih.gov/pubmed/22750884 ref]) to correct long reads (<span style="color:#0000FF;">D5</span>) with short reads (<span style="color:#0000FF;">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 firstly investigated the effect of sequencing depths on assembly ([[Read Depths]]), then set genome size in running [[pacBioToCA]], finally we tried different Celera Assembler parameters for [[runCA]].
 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>).