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After read correction, PBcR can be used to ''de novo'' assemble the genome using runCA or Mira3. |
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After read correction, PBcR can be used to ''de novo'' assemble the genome using runCA or Mira3. |
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We have assembled the genome with the all PBcR and the filtered PBcR (25X, using gatekeeper) by runCA
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We have assembled the genome with the all PBcR and the filtered PBcR (25X, using gatekeeper) by runCA.
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runCA -p asm -d asm -s asm.spec PacBio_Illumia.frg > asm.out 2>&1 |
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runCA -p asm -d asm -s asm.spec PacBio_Illumia.frg > asm.out 2>&1 |
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= Evaluation =
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We have evaluated the assemblies with [http://bioinf.spbau.ru/en/quast QUAST 2.2](reference genome and genes下載).
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{| {{table}}
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| align="center" style="background:#f0f0f0;"|'''Statistics without reference'''
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| align="center" style="background:#f0f0f0;"|'''071634_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''192221_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''210845_raw_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''071634_100X_asm.ctg'''
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| align="center" style="background:#f0f0f0;"|'''071634_118X_asm.ctg'''
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|-
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| # contigs||80||93||83||61||69
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|-
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| Largest contig||745120||664876||562203||663399||434084
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|-
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| Total length||4975695||5031560||5043217||4804004||4805579
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|-
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| N50||356974||221472||324225||295449||179662
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|-
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| Misassemblies||||||||||
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|-
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| # misassemblies||11||17||21||10||13
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|-
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| Misassembled contigs length||1552524||976207||2108892||1222277||782726
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|-
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| Mismatches||||||||||
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|-
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| # mismatches per 100 kbp||3.32||2.91||3.06||7.08||6.4
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|-
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| # indels per 100 kbp||2.98||1.38||1.01||13.15||5.2
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|-
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| # N's per 100 kbp||0.38||0.12||0.22||0.4||0.37
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|-
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| Genome statistics||||||||||
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| Genome fraction (%)||99.97||100||100||99.304||99.424
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|-
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| Duplication ratio||1.074||1.086||1.090||1.043||1.047
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|-
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| # genes||4489 + 7 part||4490 + 7 part||4495 + 2 part||4461 + 25 part||4451 + 31 part
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|-
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| NGA50||357183||221098||279423||226118||179662
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