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Self-correction approach (SCA) was proposed in the [http://www.ncbi.nlm.nih.gov/pubmed/24034426 ref] (''Reducing assembly complexity of microbial genomes with single-molecule sequencin'', Genome Biology 2013). |
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Self-correction approach (SCA) was proposed in the [http://www.ncbi.nlm.nih.gov/pubmed/24034426 ref] (''Reducing assembly complexity of microbial genomes with single-molecule sequencin'', Genome Biology 2013). |
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=Dataset 5 (''E. coli'' K-12 MG1655, 17 SMRT cells)=
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We randomly selected four, six and eight SMRT cells three times for each, and access the correctness by Quast.
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==Assembly==
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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;"|'''4 SMRT cells : 1st Set'''
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| align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set'''
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| align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set'''
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| align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 1st Set'''
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| align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set'''
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| align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set'''
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| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set'''
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| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set'''
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| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set'''
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|-
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|# contigs||5||10||4||11||7||8||6||10||5
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|Largest contig||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308
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|-
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|Total length||4 684 069||4 723 363||4 671 153||4 736 342||4 711 060||4 708 831||4 706 433||4 731 334||4 691 736
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|-
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|N50||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308
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|-
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| style="background:#f0f0f0;"| '''Misassemblies'''||||||||||||||||||
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|-
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|# misassemblies||10||13||13||15||12||11||11||16||12
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|-
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|Misassembled contigs length ||3 788 648||4 700 016||4 671 153||4 726 005||4 685 712||3 339 030||4 694 303||4 698 068||4 649 308
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|-
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| style="background:#f0f0f0;"| '''Mismatches'''||||||||||||||||||
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|-
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|# mismatches per 100kbp||0.47||0.56||0.37||0.19||0.11||0.15||0.13||0.43||0.17
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|-
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|# indels per 100kbp||1.08||4.44||0.22||1.66||0.63||0.65||0.19||4.59||0.56
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|-
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|# N's per 100kbp ||0||0||0||0||0||0||0||0||0
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|-
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| style="background:#f0f0f0;"| '''Genome Statistics'''||||||||||||||||||
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|-
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|Genome fraction(%) ||100||100||99.994||99.999||100||100||100||99.99||100
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|-
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|Duplication ratio ||1.01||1.018||1.007||1.021||1.031||1.015||1.012||1.02||1.011
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|-
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|# genes ||4495+2 part||4495+2 part||4493+3 part||4494+3 part||4495+2 part||4495+2 part||4495+2 part||4494+3 part||4495+2 part
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|-
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|NGA50 ||1 207 217||2 558 505||1 640 882||2 888 022||2 834 458||1 298 912||1 477 605||1 344 200||2 995 586
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|-
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|'''Running Time'''||?hr ?m||?hr ?m||?hr ?m||21hr 05m||19hr 32m||21hr 01m||26hr 46m|||27hr 52m||26hr 13m
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|}
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=Dataset 6 (''E.coli'' K-12 MG1655, 8 SMRT cells)= |
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=Dataset 6 (''E.coli'' K-12 MG1655, 8 SMRT cells)= |
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We used all SMRT cells and randomly selected four and six 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]]. |
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We used all SMRT cells and randomly selected four and six 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]]. |
