Version Differences for HGAP
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(→Postprocess by discarding lower-case bases)
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(→Assembly)
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| Line 684: | |||
| We used [https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-in-SMRT-Analysis HGAP3.0.xml] protocol and ran dataset 9 on SMRT portal. | We used [https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-in-SMRT-Analysis HGAP3.0.xml] protocol and ran dataset 9 on SMRT portal. | ||
| ==Assembly== | ==Assembly== | ||
| + | with different genomeSize | ||
| {| {{table}} border="1" | {| {{table}} border="1" | ||
| | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''All Data''' | + | | align="center" style="background:#f0f0f0;"|'''genomeSize=4650000''' |
| + | | align="center" style="background:#f0f0f0;"|'''genomeSize=4185000''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''genomeSize=5115000''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''genomeSize=3720000''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''genomeSize=5580000''' | ||
| |- | |- | ||
| - | |# contigs||1 | + | |# contigs||[[Media:f25_d9_all.fa | 1]]||[[Media:f25_d9_all_0.9g.fa | 1]]||[[Media:f25_d9_all_1.1g.fa | 1]]||[[Media:f25_d9_all_0.8g.fa | 1]]||[[Media:f25_d9_all_1.2g.fa | 1]] |
| + | |- | ||
| + | |Largest contig||4644061||4651184||4644056||4651207||4651348 | ||
| |- | |- | ||
| - | |Largest contig||4 655 855 | + | |Total length||4644061||4651184||4644056||4651207||4651348 |
| |- | |- | ||
| - | |Total length||4 655 855 | + | |N50||4644061||4651184||4644056||4651207||4651348 |
| |- | |- | ||
| - | |N50||4 655 855 | + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''Misassemblies''']]|||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| '''Misassemblies'''|| | + | |# misassemblies||8||8||8||8||8 |
| |- | |- | ||
| - | |# misassemblies||8 | + | |Misassembled contigs length ||4644061||4651184||4644056||4651207||4651348 |
| |- | |- | ||
| - | |Misassembled contigs length ||4 655 855 | + | | style="background:#f0f0f0;"| '''Mismatches'''|||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| '''Mismatches'''|| | + | |# mismatches per 100kbp||0.13||0.39||0.13||0.34||0.19 |
| |- | |- | ||
| - | |# mismatches per 100kbp||0.3 | + | |# indels per 100kbp||31.34||31.64||31.27||33.04||30.63 |
| |- | |- | ||
| - | |# indels per 100kbp||0.86 | + | |# N's per 100kbp ||0||0||0||0||0 |
| |- | |- | ||
| - | |# N's per 100kbp ||0 | + | | style="background:#f0f0f0;"| '''Genome Statistics'''|||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| '''Genome Statistics'''|| | + | |Genome fraction(%) ||100||99.998||100||99.998||100 |
| |- | |- | ||
| - | |Genome fraction(%) ||100 | + | |Duplication ratio ||1.001||1.003||1.001||1.003||1.003 |
| |- | |- | ||
| - | |Duplication ratio ||1.004 | + | |# genes ||4494 + 3 part||4493 + 4 part||4494 + 3 part||4493 + 4 part||4494 +3 part |
| |- | |- | ||
| - | |# genes ||4494 + 3 part | + | |NGA50 ||3025485||960375||3025483||960380||960403 |
| |- | |- | ||
| - | |NGA50 ||3 026 418 | + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||24m 50s||23m 26s||24m 25s||21m 32s||26m 5s |
| - | |- | ||
| - | |'''Running Time'''||1hr 22m | ||
| - | |- | ||
| |} | |} | ||
| ==Postprocess by discarding lower-case bases == | ==Postprocess by discarding lower-case bases == | ||