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== Evaluation ==
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* '''Benchmark genome'''
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: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptococcus_pneumoniae_TIGR4_uid57857/ S. pneumoniae TIGR4]
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* '''Evaluated by QUAST'''
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: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.3)
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: Running QUAST needs [[Media:S_pneu.ncbi|gene list]] and [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptococcus_pneumoniae_TIGR4_uid57857/ NC_003028.fna] information. There are 2301 genes in total.
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*'''Score with QUAST: With PacBio Long Reads''' [http://sb.nhri.org.tw/comps/quast/Allpaths-LG/S_pneu/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;"|'''Website Data'''
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| align="left" style="background:#f0f0f0;"|'''Raw Data'''
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|-
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| # contigs||[[Media:alg_d3_web.fasta | 1]]||[[Media:alg_d3_raw.fasta | 5]]
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|-
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| Largest contig||2162245||1340620
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|-
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| Total length||2162245||2140045
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|-
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| N50||2162245||1340620
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|-
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| align="left" style="background:#f0f0f0;"|[[Media:spades_D3.pdf | '''Misassemblies''']]
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|-
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| # misassemblies||4||1
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|-
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|Misassembled contigs length ||2162245||1340620
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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 ||5.7||2.15
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|-
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|# indels per 100kbp ||3.52||1.08
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|-
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|# N's per 100kbp ||0.05||0.14
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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 (%)||99.946||99.967
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|-
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| Duplication ratio ||1.011||1.005
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|-
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| # genes||2297 + 4 part ||2299 + 2 part
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|-
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| NGA50 ||1198037||1338442
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|-
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| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 1hr16m ||6hr 05m
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|-
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|}
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[[Media: spades_d3_summary.pdf | '''Misassemblies''']] for Adobe reader.
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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;"|'''Website Data'''
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| align="left" style="background:#f0f0f0;"|'''Raw Data'''
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|-
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| # contigs||[[Media:alg_d3_web_nopac.fasta | 4]]||[[Media:alg_d3_raw_nopac.fasta | 6]]
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|-
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| Largest contig||1663585||2135901
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|-
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| Total length||2161502||2144412
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|-
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| N50||1663585||2135901
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|-
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| align="left" style="background:#f0f0f0;"|[[Media:spdes_D3_nopac.pdf | '''Misassemblies''']]
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|-
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| # misassemblies||5||19
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|-
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|Misassembled contigs length ||1663585||2138844
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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 ||2.62||4.9
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|-
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|# indels per 100kbp ||1.5||17.33
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|-
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|# N's per 100kbp ||759.8||1714.74
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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 (%)||98.798||97.204
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|-
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| Duplication ratio ||1.022||1.019
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|-
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| # genes||2271 + 15 part ||2239 + 33 part
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|-
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| NGA50 ||403409||224016
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|-
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| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 19m ||53m
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|-
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|}
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[[Media: spades_d3_nopac_summary.pdf | '''Misassemblies''']] for Adobe reader.
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