Version Differences for Home

Revision as of 15 August 2014 19:33

(→Datasets employed in this study)

Revision as of 15 August 2014 19:34

(→Datasets employed in this study)

 = Datasets employed in this study =
 <font size=3>
-								We have used <span style="color:#FF0000;background-color:#ffffcc;">ALLPATHS-LG</span> and <span style="color:#FF0000;background-color:#ffffcc;">SPAdes 3.1</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 used <span style="color:#FF0000;background-color:#ffffcc;">ALLPATHS-LG</span> and <span style="color:#FF0000;background-color:#ffffcc;">SPAdes 3.1</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>).
 </font>
-								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 <span style="color:#0000FF;">PBcR pipeline</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]].
 </font>