Version Differences for SCA
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(→Self-correction)
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(→Self-Correction Assembly)
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| =Self-Correction Assembly= | =Self-Correction Assembly= | ||
| - | Following we used ''E. coli'' as an example to show the steps. All the necessary programs could be downloaded and more detail information from [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA PacBioToCA] | + | Following we used ''E. coli'' as an example to show the steps. All the necessary programs were downloaded from [http://www.cbcb.umd.edu/software/PBcR/closure/ cbcb]and more detail information from [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA PacBioToCA] |
| 1. Long reads self-correction | 1. Long reads self-correction | ||
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| 5. Assemble | 5. Assemble | ||
| runCA -p asm -d asm -s asm.spec 25X_Clr.frg | runCA -p asm -d asm -s asm.spec 25X_Clr.frg | ||
| =Dataset 5 (''E. coli'' K-12 MG1655, 17 SMRT cells)= | =Dataset 5 (''E. coli'' K-12 MG1655, 17 SMRT cells)= | ||
| We used all SMRT cells and randomly selected four, six and eight SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/SCA/D5/report.html more detail]) | We used all SMRT cells and randomly selected four, six and eight SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/SCA/D5/report.html more detail]) | ||