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We did assembly by SPAdes with [[Data|Dataset 4]] raw data and used [[Data|Dataset 5]], 1-4 SMRT cell subreads to scaffold by SSPACE-longread.
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We did assembly by SPAdes with [[Data|Dataset 4]] raw data and used Dataset 9 different subreads depths of [[Data|Dataset 5]] to scaffold by SSPACE-longread.
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We arbitrary chose 1-4 SMRT cells:<br> |
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We arbitrary chose 1-4 SMRT cells:<br> |
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Three single SMRT cell: m120208_071634<br>
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One single SMRT cell: m120208_071634<br>
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Two SMRT cells: m120228_210845 + m120208_122534<br> |
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Two SMRT cells: m120228_210845 + m120208_122534<br> |
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Three SMRT cells: m120228_115504 + m120228_152936 + m120228_100807<br> |
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Three SMRT cells: m120228_115504 + m120228_152936 + m120228_100807<br> |
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We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.3](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]]). |
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We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.3](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]]). |
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Single SMRT cell reads were corrected with raw, 100X and 118X short reads.
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{| {{table}} border="1" |
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{| {{table}} border="1" |
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| align="center" style="background:#f0f0f0;"|'''Statistics without reference''' |
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| align="center" style="background:#f0f0f0;"|'''Statistics without reference''' |
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| align="center" style="background:#f0f0f0;"|'''071634_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''Miseq_only'''
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| align="center" style="background:#f0f0f0;"|'''192221_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''Miseq_1cell'''
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| align="center" style="background:#f0f0f0;"|'''210845_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''Miseq_2cell'''
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| align="center" style="background:#f0f0f0;"|'''071634_100X_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''Miseq_3cell'''
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| align="center" style="background:#f0f0f0;"|'''071634_118X_asm.ctg''' |
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| align="center" style="background:#f0f0f0;"|'''071634_118X_asm.ctg''' |
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| align="center" style="background:#f0f0f0;"|'''192221_118X_asm.ctg''' |
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| align="center" style="background:#f0f0f0;"|'''192221_118X_asm.ctg''' |
