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== Sequence assembly == |
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== Sequence assembly == |
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There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOPdenovo, SPAdes 2.5, Velvet, used in the data, and the assembly results is download from [http://bioinf.spbau.ru/en/content/spades-25-gage-b-data-sets SPAdes 2.5]
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There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOPdenovo, SPAdes 2.5, Velvet, used in the data, and the assembly results were downloaded from [http://bioinf.spbau.ru/en/content/spades-25-gage-b-data-sets SPAdes 2.5]
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== Contig integrator == |
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== Contig integrator == |
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* '''Evaluated by QUAST''' |
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* '''Evaluated by QUAST''' |
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.1) |
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.1) |
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*'''Score with Mauve Assembly Metrics, N50, Blast and GAGE:'''
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{| {{table}} border="1"
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| align="center" style="background:#f0f0f0;"|'''Name'''
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| align="center" style="background:#f0f0f0;"|'''NumContigs'''
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| align="center" style="background:#f0f0f0;"|'''NumAssemblyBases'''
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| align="center" style="background:#f0f0f0;"|'''DCJ_Distance'''
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| align="center" style="background:#f0f0f0;"|'''NumMisCalled'''
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| align="center" style="background:#f0f0f0;"|'''NumUnCalled'''
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| align="center" style="background:#f0f0f0;"|'''NumGapsRef'''
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| align="center" style="background:#f0f0f0;"|'''NumGapsAssembly'''
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| align="center" style="background:#f0f0f0;"|'''TotalBasesMissed'''
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| align="center" style="background:#f0f0f0;"|'''%Missed'''
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| align="center" style="background:#f0f0f0;"|'''ExtraBases'''
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| align="center" style="background:#f0f0f0;"|'''%Extra'''
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| align="center" style="background:#f0f0f0;"|'''BrokenCDS'''
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| align="center" style="background:#f0f0f0;"|'''IntactCDS'''
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| align="center" style="background:#f0f0f0;"|'''ContigN50^'''
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| align="center" style="background:#f0f0f0;"|'''ContigN90'''
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| align="center" style="background:#f0f0f0;"|'''MaxContigLength'''
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| align="center" style="background:#eee685;"|'''N50^'''
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| align="center" style="background:#eee685;"|'''Blast_IntactCDS'''
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| align="center" style="background:#f0f0f0;"|'''Units(>200)'''
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| align="center" style="background:#f0f0f0;"|'''N50^'''
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| align="center" style="background:#f0f0f0;"|'''cor.Units'''
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| align="center" style="background:#f0f0f0;"|'''cor.N50^'''
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| align="center" style="background:#f0f0f0;"|'''Errors,(Indel>=5,Inv,Rel)'''
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|-
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| Abyss||659||2854631||590||132||6||436||499||70014||2.4117||7077||0.2479||207||2486||9223||2512||35459||9229||2305||548||9154||554||9115||7,(2,0,5)
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|-
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| Edena||3287||2557545||3143||224||1||2957||3033||390614||13.4552||15975||0.6246||784||1909||1256||359||8680||1256||1053||2679||1073||2680||1072||4,(1,0,3)
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|-
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| SOAPdenovo||674||2872327||522||85||1||482||437||71040||2.4471||10463||0.3643||154||2539||9626||3069||47607||9762||2361||509||9626||511||9626||3,(2,0,1)
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|-
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| Velvet||502||2858949||432||153||12||377||386||69466||2.3928||7682||0.2687||137||2556||12962||3811||54726||13005||2421||405||12685||422||12217||19,(10,4,5)
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|-bgcolor="#66CCFF"
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| CISA||347||2866024||330||266||15||316||278||60323||2.0779||11406||0.398||121||2572||14992||4664||54747||15327||2482||322||14916||343||14743||20,(6,5,9)
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| GAA<sup>#</sup>||1287 ||2798306 ||1166 ||191 ||6 ||1069 ||1084 ||144098 ||4.9636 ||12985 ||0.4691 ||322 ||2371 ||8319 ||2459 ||36637 ||8374||2045 ||1035 ||8209 ||1040 ||8095 ||9,(4,1,4)
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| GAA*||1150||2827068||1022||219||7||970||952||123336 ||4.24845||17517 ||0.6216||292 ||2401 ||8977 ||2614 ||38358 ||9026||2123 ||919 ||8943 ||925 ||8835 ||10,(4,2,4)
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|-
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| MAIA (split4)||4||2924771||6||127||6767||504||505||87938||3.0291||115881||3.9621||146||2547||1426408||5502||1464437||1464437||2390||-||-||-||-||-
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| MAIA (split4&n)||505||2859291||498||105||120||478||407||103565||3.5674||24695||0.8637||141||2552||12570||3840||52790||12800||2376||404||12469||401||11838||2,(1,0,1)
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| minimus2<sup>#</sup>||421 ||2863142 ||399 ||206 ||1 ||359 ||343 ||70296 ||2.4214 ||15467 ||0.5400 ||142 ||2552 ||13049 ||3951 ||50951 ||13159||2425 ||396 ||13042 ||408 ||12725 ||13,(5,2,6)
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| minimus2*||302 ||2852733 ||302 ||276 ||1 ||308 ||272 ||90585 ||3.12 ||26239 ||0.92 ||114 ||2579 ||16577 ||5117 ||54766 ||16835||2468 ||299 ||16473 ||319||15528||22,(6,7,9)
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