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Revision as of 22 August 2014 01:35

(→Datasets employed in this study)

Revision as of 22 August 2014 01:36

(→Datasets employed in this study)

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-								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 [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/wgs-package.tar.gz 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]]. <span style="color:#0000FF;">SPAdes 3.1 </span> is able to directly hybrid assemble the combined dataset (<span style="color:#0000FF;">D4+D5</span>). In addition, a scaffolder, named <span style="color:#0000FF;">[http://www.baseclear.com/lab-products/bioinformatics-tools/sspace-longread/ SSPACE-LongRead (v1-1)]</span>, was used to scaffold pre-assembled contigs constructed from short reads (<span style="color:#0000FF;">D4</span>) using long reads (<span style="color:#0000FF;">D5</span>).
+								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 [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/wgs-package.tar.gz PacBioToCA]), then to ''de novo'' assemble the corrected long reads (by [ftp://ftp.cbcb.umd.edu/pub/data/PBcR/closure_paper/wgs-package.tar.gz 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]]. <span style="color:#0000FF;">SPAdes 3.1 </span> is able to directly hybrid assemble the combined dataset (<span style="color:#0000FF;">D4+D5</span>). In addition, a scaffolder, named <span style="color:#0000FF;">[http://www.baseclear.com/lab-products/bioinformatics-tools/sspace-longread/ SSPACE-LongRead (v1-1)]</span>, was used to scaffold pre-assembled contigs constructed from short reads (<span style="color:#0000FF;">D4</span>) using long reads (<span style="color:#0000FF;">D5</span>).
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