Version Differences for SSPACE

Line 1:
    + = Evaluation =  
    + We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.2](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]]).  
       
    + Single SMRT cell reads were corrected with raw, 100X and 118X short reads.  
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''192221_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''210845_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''192221_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''210845_118X_asm.ctg'''  
    + |-  
    + | # contigs||80||93||83||61||69||68||66  
    + |-  
    + | Largest contig||745120||664876||562203||663399||434084||345313||437164  
    + |-  
    + | Total length||4975695||5031560||5043217||4804004||4805579||4801310||4733683  
    + |-  
    + | N50||356974||221472||324225||295449||179662||207976||186993  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||||  
    + |-  
    + | # misassemblies||11||17||21||10||13||20||15  
    + |-  
    + | Misassembled contigs length||1552524||976207||2108892||1222277||782726||1156917||527873  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||3.32||2.91||3.06||7.08||6.4||10.33||4.13  
    + |-  
    + | # indels per 100 kbp||2.98||1.38||1.01||13.15||5.2||5.54||2.69  
    + |-  
    + | # N's per 100 kbp||0.38||0.12||0.22||0.4||0.37||0.4||0.23  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||||  
    + |-  
    + | Genome fraction (%)||99.97||100||100||99.304||99.424||99.522||98.712  
    + |-  
    + | Duplication ratio||1.074||1.086||1.090||1.043||1.047||1.04||1.033  
    + |-  
    + | # genes||4489 + 7 part||4490 + 7 part||4495 + 2 part||4461 + 25 part||4451 + 31 part||4459 + 28 part||4412 + 32 part  
    + |-  
    + | NGA50||357183||221098||279423||226118||179662||194634||191457  
    + |-  
    + |}  
       
    + We discarded the contigs which fewer than 100 reads aligned. [http://sb.nhri.org.tw/comps/quast/ReadDepths/1_SMRT/report.html more detail]  
       
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''192221_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''210845_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''071634_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''192221_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''210845_118X_asm.ctg'''  
    + |-  
    + | # contigs||[[Media:071634_raw_asm.ctg.fa|19]]||[[Media:192221_raw_asm.ctg.fa|24]]||[[Media:210845_raw_asm.ctg.fa|21]]||[[Media:071634_100X_asm.ctg.fa|28]]||[[Media:071634_118X_asm.ctg.fa|38]]||[[Media:192221_118X_asm.ctg.fa|29]]||[[Media:210845_118X_asm.ctg.fa|31]]  
    + |-  
    + | Largest contig||745120||664876||592203||663399||434084||345313||437164  
    + |-  
    + | Total length||4669108||4675696||4700617||4636263||4644391||4603072||4578972  
    + |-  
    + | N50||356974||222559||399011||295449||180706||207976||191458  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||||  
    + |-  
    + | # misassemblies||7||6||11||6||5||7||6  
    + |-  
    + | Misassembled contigs length||1539749||936587||2058922||1200212||727024||1097466||478971  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.75||2.75||3.04||7.08||5.85||8.82||3.69  
    + |-  
    + | # indels per 100 kbp||2.23||1.1||1.17||13.46||5.83||2.49||2.37  
    + |-  
    + | # N's per 100 kbp||0.19||0.02||0.04||0.26||0.15||0.07||0.02  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||||  
    + |-  
    + | Genome fraction (%)||99.639||99.699||99.834||99.984||99.051||98.78||98.159  
    + |-  
    + | Duplication ratio||1.011||1.011||1.017||1.01||1.015||1.005||1.006  
    + |-  
    + | # genes||4473 + 15 part||4465 + 18 part||4480 + 10 part||4435 + 29 part||4431 + 36 part||4413 + 36 part||4380 + 34 part  
    + |-  
    + | NGA50||357183||221098||279423||226118||179662||194634||191457  
    + |-  
    + |}  
       
       
    + Two SMRT cell reads were corrected with raw, 100X, and 118X short reads. The PBcR were then filtered to 25X or directly assembled by runCA.  
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||106||80||81||71||81||54  
    + |-  
    + | Largest contig||762045||757702||767781||405645||520095||570062  
    + |-  
    + | Total length||5168000||5080370||4918962||4799524||4832961||4725680  
    + |-  
    + | N50||419161||405539||331262||193986||186504||210927  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||13||18||15||9||16||16  
    + |-  
    + | Misassembled contigs length||1591856||1751860||1703983||165469||616747||1468075  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.44||1.83||5.08||4.34||6.28||6.08  
    + |-  
    + | # indels per 100 kbp||0.88||0.82||6.34||2.14||5.61||2.93  
    + |-  
    + | # N's per 100 kbp||0.48||0.04||0.94||0.02||0.43||0.08  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||100||100||99.652||98.76||99.567||99.194  
    + |-  
    + | Duplication ratio||1.116||1.098||1.065||1.048||1.047||1.028  
    + |-  
    + | # genes||4495 + 2 part||4495 + 2 part||4475 + 16 part||4432 + 31 part||4458 + 30 part||4434 + 43 part  
    + |-  
    + | NGA50||418393||405538||235822||193833||194196||199657  
    + |-  
    + |}  
       
    + We discarded the contigs which fewer than 100 reads aligned. [http://sb.nhri.org.tw/comps/quast/ReadDepths/2_SMRT/report.html more detail]  
       
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''2_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||[[Media:2_raw_asm.ctg.fa|16]]||[[Media:2_raw_25X_asm.ctg.fa|17]]||[[Media:2_100X_asm.ctg.fa|22]]||[[Media:2_100X_25X_asm.ctg.fa|33]]||[[Media:2_118X_asm.ctg.fa|35]]||[[Media:2_118X_25X_asm.ctg.fa|32]]  
    + |-  
    + | Largest contig||762045||757702||767781||405645||520095||570062  
    + |-  
    + | Total length||4650035||4675233||4651814||4574523||4648591||4588060  
    + |-  
    + | N50||514903||405539||331262||193986||194625||223426  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||4||6||10||4||5||8  
    + |-  
    + | Misassembled contigs length||1564680||1697372||1683620||141677||569893||1424613  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.43||2.23||4.94||1.8||5.56||5.97  
    + |-  
    + | # indels per 100 kbp||1.76||0..84||6.19||1.8||4.48||2.86  
    + |-  
    + | # N's per 100 kbp||0.06||0||0.26||0||0.13||0.04  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||99.371||99.633||99.536||98.364||99.163||98.603  
    + |-  
    + | Duplication ratio||1.006||1.013||1.009||1.003||1.011||1.004  
    + |-  
    + | # genes||4458 + 13 part||4466 + 8 part||4462 + 22 part||4404 + 39 part||4438 + 32 part||4405 + 42 part  
    + |-  
    + | NGA50||418393||405538||235822||193833||194196||199657  
    + |-  
    + |}  
       
       
    + Three SMRT cells reads were corrected with raw, 100X, and 118 short reads. The PBcR were then filtered to 25X or directly assembled by runCA.  
    + {| {{table}} border=1"1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||219||74||98||32||86||39  
    + |-  
    + | Largest contig||771076||1426293||981874||822480||1091515||520962  
    + |-  
    + | Total length||5873961||5171438||5051244||4730819||4906749||4668968  
    + |-  
    + | N50||247798||317846||413464||600008||286035||218547  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||25||10||22||8||25||11  
    + |-  
    + | Misassembled contigs length||1361077||1372143||2201123||1855654||1800186||1350243  
    + |-  
    + | Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||4.03||2.5||2.030||1.5||4.71||5.45  
    + |-  
    + | # indels per 100 kbp||1.68||0.97||5.64||3.3||4.13||3.86  
    + |-  
    + | # N's per 100 kbp||0.34||0.140||0.46||0.11||0.18||0.02  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||100||100||99.733||99.197||99.69||98.93  
    + |-  
    + | Duplication ratio||1.268||1.116||1.092||1.028||1.063||1.018  
    + |-  
    + | # genes||4494 + 3 part||4495 + 2 part||4484 + 9 part||4460 + 19 part||4468 + 20 part||4427 + 35 part  
    + |-  
    + | NGA50||286997||323732||348693||599239||286035||193471  
    + |-  
    + |}  
       
    + We discarded the contigs which fewer than 100 reads aligned. [http://sb.nhri.org.tw/comps/quast/ReadDepths/3_SMRT/report.html more detail]  
       
    + {| {{table}} border=1"1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''3_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||[[Media:3_raw_asm.ctg.fa|29]]||[[Media:3_raw_25X_asm.ctg.fa|15]]||[[Media:3_100X_asm.ctg.fa|20]]||[[Media:3_100X_25X_asm.ctg.fa|18]]||[[Media:3_118X_asm.ctg.fa|27]]||[[Media:3_118X_25X_asm.ctg.fa|29]]  
    + |-  
    + | Largest contig||771076||1426293||981876||822480||1091515||520962  
    + |-  
    + | Total length||4672216||4666874||4656670||4613610||4650236||4593856  
    + |-  
    + | N50||316212||323732||413464||600008||286035||218547  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||6||4||10||6||7||7  
    + |-  
    + | Misassembled contigs length||1270144||1321332||2130162||1844194||1736227||1326538  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.07||2.14||1.67||1.48||4.35||5.09  
    + |-  
    + | # indels per 100 kbp||0.98||0.65||5.54||3.31||2.88||3.76  
    + |-  
    + | # N's per 100 kbp||0.06||0||0.17||0.02||0.04||0  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||99.037||99.636||99.615||99.087||99.478||98.614  
    + |-  
    + | Duplication ratio||1.017||1.01||1.008||1.004||1.009||1.005  
    + |-  
    + | # genes||4439 + 24 part||4467 + 11 part||4472 + 19 part||4454 + 22 part||4457 + 21 part||4410 + 35 part  
    + |-  
    + | NGA50||286997||323732||348693||599239||286035||193471  
    + |-  
    + |}  
       
       
    + Four SMRT cell reads were corrected with raw, 100X, and 118X short reads. The PBcR were then filtered to 25X or directly assembled by runCA.  
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''4_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||286||51||123||23||71||40  
    + |-  
    + | Largest contig||532128||1812746||688723||1257198||983533||621920  
    + |-  
    + | Total length||6162978||5045811||5144868||4693193||4862387||4665855  
    + |-  
    + | N50||147254||834736||398131||694380||412226||285200  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||24||13||26||8||31||13  
    + |-  
    + | Misassembled contigs length||800651||3633076||2341550||2708632||2412628||1302367  
    + |-  
    + | Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||3.41||2.240||5.060||1.93||4.45||7.3  
    + |-  
    + | # indels per 100 kbp||1.36||0.97||5.21||3.82||4.08||5.71  
    + |-  
    + | # N's per 100 kbp||1.2||0.16||0.39||0.04||0.41||0  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||100||100||99.74||99.337||99.798||98.559  
    + |-  
    + | Duplication ratio||1.331||1.089||1.112||1.019||1.052||1.022  
    + |-  
    + | # genes||4495 + 2 part||4494 + 3 part||4482 + 10 part||4470 + 9 part||4481 + 12 part||4413 + 36 part  
    + |-  
    + | NGA50||182232||476726||317322||694380||286770||214828  
    + |-  
    + |}  
       
    + We discarded the contigs which fewer than 100 reads aligned. [http://sb.nhri.org.tw/comps/quast/ReadDepths/4_SMRT/report.html more detail]  
       
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Statistics without reference'''  
    + | align="center" style="background:#f0f0f0;"|'''4_raw_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_raw_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_100X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_100X_25X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_118X_asm.ctg'''  
    + | align="center" style="background:#f0f0f0;"|'''4_118X_25X_asm.ctg'''  
    + |-  
    + | # contigs||[[Media:4_raw_asm.ctg.fa|40]]||[[Media:4_raw_25X_asm.ctg.fa|12]]||[[Media:4_100X_asm.ctg.fa|21]]||[[Media:4_100X_25X_asm.ctg.fa|12]]||[[Media:4_118X_asm.ctg.fa|21]]||[[Media:4_118X_25X_asm.ctg|26]]  
    + |-  
    + | Largest contig||532128||1812746||688723||1257198||983533||621920  
    + |-  
    + | Total length||4726973||4659487||4656544||4602600||4654299||4508804  
    + |-  
    + | N50||180844||834736||398131||1071366||412226||285200  
    + |-  
    + | style="background:#f0f0f0;"| Misassemblies||||||||||||  
    + |-  
    + | # misassemblies||7||8||8||6||15||9  
    + |-  
    + | Misassembled contigs length||736689||3595196||2252884||2698687||2362706||1274915  
    + |-  
    + | style="background:#f0f0f0;"| Mismatches||||||||||||  
    + |-  
    + | # mismatches per 100 kbp||2.35||2.28||2.53||2||4.41||6.26  
    + |-  
    + | # indels per 100 kbp||0.87||0.75||3.94||3.81||3.31||4.49  
    + |-  
    + | # N's per 100 kbp||0.17||0.13||0.02||0.04||0.04||0  
    + |-  
    + | style="background:#f0f0f0;"| Genome statistics||||||||||||  
    + |-  
    + | Genome fraction (%)||99.193||99.215||99.62||98.967||99.687||97.023  
    + |-  
    + | Duplication ratio||1.028||1.012||1.008||1.003||1.009||1.003  
    + |-  
    + | # genes||4443 + 26 part||4456 + 12 part||4474 + 17 part||4452 + 11 part||4474 + 15 part||4344 + 37 part  
    + |-  
    + | NGA50||182232||476726||317322||694380||286770||247828  
    + |-  
    + |}