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OVERWRITE=True\ |
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OVERWRITE=True\ |
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| tee prepare.out |
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| tee prepare.out |
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== Evaluation ==
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* '''Benchmark genome'''
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: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/ R. sphaeroides 2.4.1]
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* '''Evaluated by QUAST'''
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.2)
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: Running QUAST needs [[Media:R_sphaeroides.ncbi.gz|gene]] and [[Media:R_sphaeroides.fna.gz|sequence]] information. There are 4438 genes in total.
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*'''Score with QUAST: With PacBio Long Reads''' more detail
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{| {{table}} border="１"
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| align="left" style="background:#f0f0f0;"|'''Basic statistics'''
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| align="left" style="background:#f0f0f0;"|'''Raw Data'''
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| align="left" style="background:#f0f0f0;"|'''Website Data'''
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| align="left" style="background:#f0f0f0;"|'''Self-fraction Data'''
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| align="left" style="background:#f0f0f0;"|'''100 Coverage'''
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|-
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| # contigs||13||11||10||11
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|-
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| Largest contig||3188540||3188818||3188847||3188802
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|-
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| Total length||4588701||4601792||4609235||4601762
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|-
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| N50||3188540||3188818||3188847||3188802
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|-
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| align="left" style="background:#f0f0f0;"|'''Misassemblies'''
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|-
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| # misassemblies||12||16||20||19
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|-
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|Misassembled contigs length ||4361060||4370092||4557570||4484253
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|-
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| align="left" style="background:#f0f0f0;"|'''Mismatches'''
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|-
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|# mismatches per 100kbp ||3.77||3.48||4.8||6.43
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|-
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|# indels per 100kbp ||5.13||3.52||4.87||5.61
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|-
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|# N's per 100kbp ||0.09||0||0.13||0.07
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|-
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| align="left" style="background:#f0f0f0;"|'''Genome statistics'''
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|-
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| Genome fraction (%)||99.683||99.932||99.948||99.945
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|-
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| Duplication ratio ||1.005||1.011||1.009||1.007
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|-
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| # genes||4369 + 10 part ||4381 + 6 part ||4380+ 7 part ||4378 + 8 part
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|-
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| NGA50 || 2938269 || 904505 || 2715665 || 3170709
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|-
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|}
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*'''Score with QUAST: Without PacBio Long Reads ''' more detail
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{| {{table}} border="１"
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| align="left" style="background:#f0f0f0;"|'''Basic statistics'''
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| align="left" style="background:#f0f0f0;"|'''Raw Data'''
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| align="left" style="background:#f0f0f0;"|'''Website Data'''
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| align="left" style="background:#f0f0f0;"|'''Self-fraction Data'''
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| align="left" style="background:#f0f0f0;"|'''100 Coverage'''
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|-
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| # contigs||57||31||32||26
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|-
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| Largest contig||3186675||3188995||1674993||3190277
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|-
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| Total length||4583750||4592561||4620837||4607723
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|-
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| N50||3186675||3188995||1492665||3190277
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|-
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| align="left" style="background:#f0f0f0;"|'''Misassemblies'''
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|-
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| # misassemblies||6||9||17||27
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|-
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|Misassembled contigs length ||4147900||4205887||2637662||4422750
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|-
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| align="left" style="background:#f0f0f0;"|'''Mismatches'''
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|-
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|# mismatches per 100kbp ||4.23||5.81||7.49||10.76
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|-
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|# indels per 100kbp ||3.57||5.64||4.72||8.94
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|-
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|# N's per 100kbp ||149.31||120.74||197.84||812.74
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|-
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| align="left" style="background:#f0f0f0;"|'''Genome statistics'''
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|-
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| Genome fraction (%)||98.789||99.45||99.468||98.896
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|-
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| Duplication ratio ||1.022||1.018||1.015||1.02
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|-
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| # genes||4313 + 47 part ||4348 + 27 part ||4343 + 31 part ||4266 + 101 part
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|-
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| NGA50 ||3180491||3182258||1487141||546353
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|-
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|}
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