Hi all,
Recently I used MyPro tool (10.1016/j.mimet.2015.04.006) for assembly of a prokaryotic genome. In brief, assembly was carried out with different kmer using Abyss, Soap de novo, Velvet and Spades. I added an assembly from GS de novo assembler(Newbler). All these five assemblies were then integrated using CISA.
The problem rises when I map my reads to this final assembly form CISA. Some contigs (7) are such which got 0 reads mapped to it. Some other contigs (40% of contigs) are such which are covered less than 90% during mapping. Mapping was done using CLC genomics workbench and GS reference mapper. Both these mapper showed similar results. Overall, 99% reads are mapped to contigs.
So, is there any problem with MyPro tool or just CISA in general or problem lies with assemblers? Has anyone else faced the same issue?
Any assistance appreciated. Cheers
Recently I used MyPro tool (10.1016/j.mimet.2015.04.006) for assembly of a prokaryotic genome. In brief, assembly was carried out with different kmer using Abyss, Soap de novo, Velvet and Spades. I added an assembly from GS de novo assembler(Newbler). All these five assemblies were then integrated using CISA.
The problem rises when I map my reads to this final assembly form CISA. Some contigs (7) are such which got 0 reads mapped to it. Some other contigs (40% of contigs) are such which are covered less than 90% during mapping. Mapping was done using CLC genomics workbench and GS reference mapper. Both these mapper showed similar results. Overall, 99% reads are mapped to contigs.
So, is there any problem with MyPro tool or just CISA in general or problem lies with assemblers? Has anyone else faced the same issue?
Any assistance appreciated. Cheers