mis-assembl ratio in the denovo genome

[fly005304]

Hi,
In our genome project, one of the reviewer want to know the mis-assembl ratio. Our genome was assembled by soap based on solexa reads and its insert size is from 170b,500bp,800bp,2k,5K,10k,20k. Dose any one know how to evalue it, welcome any suggestions!
fly

[pmiguel]

Hi,
In our genome project, one of the reviewer want to know the mis-assembl ratio. Our genome was assembled by soap based on solexa reads and its insert size is from 170b,500bp,800bp,2k,5K,10k,20k. Dose any one know how to evalue it, welcome any suggestions!
fly

Some possibilities here (PDF) or here (HTML).

Bioinformatics (2013) 29 (23): 2959-2963. doi: 10.1093/bioinformatics/btt525

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Phillip

[flxlex]

Assembly evaluation tools will help you - some of these are mentioned in the link from @pmiguel. My list:
- FRCBAM https://github.com/vezzi/FRC_align
- REAPR http://genomebiology.com/2013/14/5/R47
- GAEMR http://www.broadinstitute.org/software/gaemr/

All these only gives estimates of the errors, and I don't even know what I would consider the ' mis-assembly ratio'...