| Line 1: |
| |
|
+ |
== Evaluation ==
|
| |
|
|
|
| |
|
+ |
* '''Benchmark genome'''
|
| |
|
|
|
| |
|
+ |
: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/ R. sphaeroides 2.4.1]
|
| |
|
|
|
| |
|
+ |
* '''Evaluated by QUAST'''
|
| |
|
+ |
: [http://bioinf.spbau.ru/en/quast/ QUAST] (QUAST v2.3)
|
| |
|
+ |
: Running QUAST requires [[Media:R_sphaeroides.ncbi|gene list]] and [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/ reference genome]. There are 4388 genes in total.
|
| |
|
|
|
| |
|
+ |
*'''Score with QUAST: With PacBio Long Reads''' [more detail]
|
| |
|
|
|
| |
|
+ |
{| {{table}} border="１"
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Basic statistics'''
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Website Data'''
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Raw Data'''
|
| |
|
+ |
|-
|
| |
|
+ |
| # contigs||[[Media:spd_d2_web.fasta | 11]]||[[Media:spd_d2_raw.fasta | 13]]
|
| |
|
+ |
|-
|
| |
|
+ |
| Largest contig||3188818||3188540
|
| |
|
+ |
|-
|
| |
|
+ |
| Total length||4601792||4588701
|
| |
|
+ |
|-
|
| |
|
+ |
| N50||3188818||3188540||3188847
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|[[Media: spades_D2.pdf | '''Misassemblies''']]
|
| |
|
+ |
|-
|
| |
|
+ |
| # misassemblies||16||12
|
| |
|
+ |
|-
|
| |
|
+ |
|Misassembled contigs length ||4370092||4361060
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Mismatches'''
|
| |
|
+ |
|-
|
| |
|
+ |
|# mismatches per 100kbp ||3.48||3.77
|
| |
|
+ |
|-
|
| |
|
+ |
|# indels per 100kbp ||3.52||5.13|
|
| |
|
+ |
|-
|
| |
|
+ |
|# N's per 100kbp ||0||0.09
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Genome statistics'''
|
| |
|
+ |
|-
|
| |
|
+ |
| Genome fraction (%)||99.932||99.683|
|
| |
|
+ |
|-
|
| |
|
+ |
| Duplication ratio ||1.011||1.005
|
| |
|
+ |
|-
|
| |
|
+ |
| # genes||4381 + 6 part ||4369 + 10 part
|
| |
|
+ |
|-
|
| |
|
+ |
| NGA50 || 904505 || 2938269
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 2hr12m ||5hr 09m
|
| |
|
+ |
|-
|
| |
|
+ |
|}
|
| |
|
+ |
[[Media: spades_d2_summary.pdf | '''Misassemblies''']] for Adobe reader.
|
| |
|
|
|
| |
|
|
|
| |
|
|
|
| |
|
+ |
*'''Score with QUAST: Without PacBio Long Reads ''' [http://sb.nhri.org.tw/comps/quast/Allpaths-LG/R_spha_nopac/report.html more detail]
|
| |
|
+ |
{| {{table}} border="１"
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Basic statistics'''
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Website Data'''
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Raw Data'''
|
| |
|
+ |
|-
|
| |
|
+ |
| # contigs||[[Media:spd_d2_web_nopac.fasta | 31]]||[[Media:spd_d2_raw_nopac.fasta | 57]]
|
| |
|
+ |
|-
|
| |
|
+ |
| Largest contig||3188995||3186675
|
| |
|
+ |
|-
|
| |
|
+ |
| Total length||4592561||4583750
|
| |
|
+ |
|-
|
| |
|
+ |
| N50||3188995||3186675
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|[[Media: spades_D2_nopac,pdf | '''Misassemblies''']]
|
| |
|
+ |
|-
|
| |
|
+ |
| # misassemblies||9||6
|
| |
|
+ |
|-
|
| |
|
+ |
|Misassembled contigs length ||4205887||4147900
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Mismatches'''
|
| |
|
+ |
|-
|
| |
|
+ |
|# mismatches per 100kbp ||5.81||4.233
|
| |
|
+ |
|-
|
| |
|
+ |
|# indels per 100kbp ||5.64||3.57
|
| |
|
+ |
|-
|
| |
|
+ |
|# N's per 100kbp ||120.74||149.31
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|'''Genome statistics'''
|
| |
|
+ |
|-
|
| |
|
+ |
| Genome fraction (%)||99.45||98.789
|
| |
|
+ |
|-
|
| |
|
+ |
| Duplication ratio ||1.018||1.022
|
| |
|
+ |
|-
|
| |
|
+ |
| # genes||4348 + 27 part ||4313 + 47 part
|
| |
|
+ |
|-
|
| |
|
+ |
| NGA50 ||3182258||3180491
|
| |
|
+ |
|-
|
| |
|
+ |
| align="left" style="background:#f0f0f0;"|''' Running Time '''|| 41m ||1hr 01m || 36m|| 19m || 33m
|
| |
|
+ |
|-
|
| |
|
+ |
|}
|
| |
|
+ |
[[Media: spades_d2_nopac_summary.pdf | '''Misassemblies''']] for Adobe reader.
|
