Version Differences for HGAP

Revision as of 22 August 2014 01:11

(→Postprocess by discarding lower-case bases)

Revision as of 22 August 2014 01:15

(→Postprocess by discarding lower-case bases)

 We used HGAP3.0.xml protocol
 								==Assembly==
 								{| {{table}} border="1"
 								| align="center" style="background:#f0f0f0;"|'''Statistics without reference '''
 								| align="center" style="background:#f0f0f0;"|'''All Data'''
 								|-
 								|# contigs||1
 								|-
 								|Largest contig||4 655 855
 								|-
 								|Total length||4 655 855
 								|-
 								|N50||4 655 855
 								|-
 								| style="background:#f0f0f0;"| '''Misassemblies'''||
 								|-
 								|# misassemblies||8
 								|-
 								|Misassembled contigs length ||4 655 855
 								|-
 								| style="background:#f0f0f0;"| '''Mismatches'''||
 								|-
 								|# mismatches per 100kbp||0.3
 								|-
 								|# indels per 100kbp||0.86
 								|-
 								|# N's per 100kbp ||0
 								|-
 								| style="background:#f0f0f0;"| '''Genome Statistics'''||
 								|-
 								|Genome fraction(%) ||100
 								|-
 								|Duplication ratio ||1.004
 								|-
 								|# genes ||4494 + 3 part
 								|-
 								|NGA50 ||3 026 418
 								|-
 								|'''Running Time'''||1hr 22m
 								|-
 								|}
 								==Postprocess by discarding lower-case bases ==
 								We discarded low quality bases which present in lower-case from contigs two-side ends. [http://sb.nhri.org.tw/comps/quast/Non-hybrid/HGAP/D7/report.html more detail]
 								{| {{table}} border="1"
 								| align="center" style="background:#f0f0f0;"|'''Statistics without reference '''
 								| align="center" style="background:#f0f0f0;"|'''All Data'''
 								|-
 								|# contigs||[[Media:hgap3_d9_all.fa | 3]]
 								|-
 								|Largest contig||4 652 541
 								|-
 								|Total length||4 652 541
 								|-
 								|N50||4 652 541
 								|-
 								| style="background:#f0f0f0;"| [[Media: HGAP_D7.pdf | '''Misassemblies''']]||
 								|-
 								|# misassemblies||8
 								|-
 								|Misassembled contigs length ||4 652 541
 								|-
 								| style="background:#f0f0f0;"| '''Mismatches'''||
 								|-
 								|# mismatches per 100kbp||0.19
 								|-
 								|# indels per 100kbp||0.56
 								|-
 								|# N's per 100kbp ||0
 								|-
 								| style="background:#f0f0f0;"| '''Genome Statistics'''||
 								|-
 								|Genome fraction(%) ||100
 								|-
 								|Duplication ratio ||1.004
 								|-
 								|# genes ||4494+3 part
 								|-
 								|NGA50 ||3 026 418
 								|-
 								|}