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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/Escherichia_coli_K_12_substr__MG1655_uid57779/ E. coli MG1655]
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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 4497 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||14||1||1||1
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|-
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| Largest contig||4625005||4638970||4638970||4638970
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|-
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| Total length||4652215||4638970||4638970||4638970
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|-
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| N50||4625005||4638970||4638970||4638970
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|-
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| align="left" style="background:#f0f0f0;"|'''Misassemblies'''
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|-
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| # misassemblies||5||1||1||1
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|-
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|Misassembled contigs length ||4625005||4638970||4638970||4638970
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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 ||1.06||0.11||0.06||0.06
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|-
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|# indels per 100kbp ||0.61||0.09||0.09||0.11
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|-
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|# N's per 100kbp ||282.94||0||0||0
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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 (%)||99.418||99.983||99.983||99.983
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|-
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| Duplication ratio ||1.013||1||1||1
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|-
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| # genes||4471 + 2 part ||4494 + 1 part ||4494 + 1 part ||4495 + 0 part
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|-
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| NGA50 || 2714032 || 4638970 || 3763133 || 4032768
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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||1||2||5||3
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|-
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| Largest contig||4633080||4631220||4575759||4560636
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|-
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| Total length||4633080||4633146||4698903||4713335
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|-
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| N50||4633080||4631220||4575759||4590636
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|-
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| align="left" style="background:#f0f0f0;"|'''Misassemblies'''
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|-
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| # misassemblies||7||3||8||8
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|-
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|Misassembled contigs length ||4633080||4631220||4577746||4711603
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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 ||1.42||1.19||2.84||1.89
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|-
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|# indels per 100kbp ||0.83||1.13||3.26||0.61
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|-
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|# N's per 100kbp ||1545.02||533.22||698.87||801.7
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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 (%)||98.343||99.345||99.265||99.284
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|-
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| Duplication ratio ||1.016||1.012||1.021||1.028
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|-
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| # genes||4395 + 31 part ||4465 + 11 part ||4460 + 14 part ||4459 + 9 part
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|-
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| NGA50 ||687701||3180483||654008||1295677
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|-
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|}
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