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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 v2.1)
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: Running QUAST needs [[Media:R_sphaeroides.ncbi.gz|gene]] and [[Media:R_sphaeroides.fna.gz|sequence]] information. There are 4388 genes in total.
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*'''Score with QUAST:''' [http://sb.nhri.org.tw/Quast/R_sphaeroides/report.html 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;"|'''ABySS'''
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| align="left" style="background:#f0f0f0;"|'''CABOD'''
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| align="left" style="background:#f0f0f0;"|'''MaSuRCA'''
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| align="left" style="background:#f0f0f0;"|'''SGA'''
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| align="left" style="background:#f0f0f0;"|'''SOAPdenovo'''
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| align="left" style="background:#f0f0f0;"|'''SPAdes 2.5'''
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| align="left" style="background:#f0f0f0;"|'''Velvet'''
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| align="left" style="background:#66CCFF;"|'''CISA'''
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|-
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| # contigs||382||131||52||733||185||40||143||'''''35'''''
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|-
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| Largest contig||71578||177098||241348||44874||204500||739647||236829||'''''740054'''''
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|-
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| Total length||4503182||3953489||4247061||4091078||4549335||4781613||4526809||'''''4950301'''''
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|-
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| NG50||21441||40287||144812||7971||45133||518052||85272||'''''523557'''''
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|-
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| align="left" style="background:#f0f0f0;"|'''Misassemblies'''
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|-
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| # misassemblies||2||6||5||0||3||9||17||'''''24'''''
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|-
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|Misassembled contigs length ||24651 ||135726 ||40523 ||0 ||24631 ||1180527 ||564277 ||'''''1850338'''''
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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 (%)||97.529||85.608||91.915||87.77||98.068||99.37||97.437||'''''99.474'''''
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|-
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| # genes||4030 + 275 part ||3685 + 128 part ||4036 + 38 part ||3348 + 592 part ||4046 + 307 part ||4347 + 23 part ||4068 + 265 part ||'''''4358 + 19 part '''''
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|-
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| # mismatches per 100 kbp ||4.83||10.51||12.48||3.22||5.98||5.82||13.11||'''''6.42'''''
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|-
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| # indels per 100 kbp ||3.43||7.97||5.84||3.34||3.9||3.63||8.34||'''''3.69'''''
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|-
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| # N's per 100kbp ||0||20.77||4.83||0||139.23||0||739.09||''''' 3.68'''''
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|-
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|}
|
