Version Differences for E. coli 36 bp
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| : As can be seen here, CISA can successfully integrate the sets of contigs and reduce the number of contigs. However, in comparison with integrating assemblies generated from different assemblers (Set 1), varying assemble parameters is less efficient (in the case of Set 2 or Set3) in completing the genome. | : As can be seen here, CISA can successfully integrate the sets of contigs and reduce the number of contigs. However, in comparison with integrating assemblies generated from different assemblers (Set 1), varying assemble parameters is less efficient (in the case of Set 2 or Set3) in completing the genome. | ||
| - | *'''Scaffold the contigs using SSPACE''' | ||
| - | : Since we have the paired-end reads of ''E. coli'', it is possible to assess the order, distance and orientation of contigs and combine them into scaffolds. We, therefore, used [http://www.ncbi.nlm.nih.gov/pubmed/21149342 SSPACE] to scaffold the contigs and quantified the scaffolds by Mauve assembly metrics. | ||
| - | {| {{table}} border="1" | ||
| - | | align="center" style="background:#f0f0f0;"|'''Name''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumContigs''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumAssemblyBases''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''DCJ_Distance''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumMisCalled''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumUnCalled''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumGapsRef''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''NumGapsAssembly''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''TotalBasesMissed''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''%Missed''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''ExtraBases''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''%Extra''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''BrokenCDS''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''IntactCDS''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''ContigN50''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''MaxContigLength''' | ||
| - | | align="center" style="background:#eee685;"|'''Blast_IntactCDS''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''Units(>200)''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''N50''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''cor.Units''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''cor.N50''' | ||
| - | | align="center" style="background:#f0f0f0;"|'''Errors,(Indel>=5,Inv,Rel)''' | ||
| - | |- | ||
| - | | CISA+SSPACE||61||4628707||68||362||188||91||93||50162||1.0812||37845||0.8176||45||4275||135136||323055||4276||61||150749||82||113511||17,(9,1,7) | ||
| - | |- | ||
| - | | Abyss+SSPACE||97||4628151||81||341||685||114||111||54656||1.178||33130||0.7158||56||4264||126232||289699||4259||85||134584||108||96149||27,(16,1,10) | ||
| - | |- | ||
| - | | Abyss scaffolding||74||4647910||68||363||296||81||82||40826||0.8799||40157||0.864||50||4270||133908||316093||4266||65||135136||78||113739||15,(6,1,8) | ||
| - | |- | ||
| - | | minimus2+SSPACE||62||4608909||64||407||219||112||86||65837||1.419||31972||0.6937||49||4271||150458||417726||4262||61||177539||78||119105||16,(8,3,5) | ||
| - | |- | ||
| - | |} | ||
| - | : The results show: | ||
| - | # The integrated contigs output by CISA can be scaffolded by SSPACE to a limited extent (from 72 to 61), which suggests that our CISA can indeed integrate the sequence information from different assemblies. | ||
| - | # To introduce the paired-end reads to the pre-assembled contigs generated by Abyss using SSPACE (Abyss+SSPACE) can only reduce the number of contigs from 133 to 97, smaller than the effect made by CISA (from 133 to 72), which suggests that contig integration prior to scaffolding can further enhance the result. | ||
| - | # The problem of misassembled contigs generated by minimus2 is not yet solved by SSPACE, which suggests that we should integrate contigs with caution. | ||