On Friday I posted a reply to a thread on SEQanswers about CEGMA. I thought I'd include a modified version of that response here as it is an issue that gets raised fairly frequently. It concerns the 'complete' and 'partial' results that CEGMA includes in the final output file that it generates (typically called 'output.completeness_report'). Here were the two questions that were posted:

1) If a partial score is higher than a complete score then does this indicate that the assembly is fragmented?
2) Also, should the partial score be lower than the complete score in an ideal situation?

Remember, these are not scores per se. Both of these figures describe a number of core eukaryotic genes (CEGs) that the CEGMA pipeline predicts to be present in the input assembly file. The 'complete' set refers to those gene predictions which CEGMA classes as 'full-length'. Note that even if CEGMA says something is 'complete' there is still the possibility that parts of the protein is missing.

This is because CEGMA is taking each CEG that it has predicted and aligns the protein sequence of that CEG to the HMM profile generated from the corresponding core gene family (made up of six proteins from Schizosacchromyces pombe, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and Homo sapiens). As I recall from memory, if the alignment spans more than 70% of the protein profile the CEG is considered to be 'complete'. This 70% threshold is an arbitrary cut-off, but seems to work well in finding genuine orthologs of CEGs.

Somewhat confusingly, although we consider 'partial' matches to be those below 70% (but above some unspecified minimum score), the output in output.completeness_report uses 'partial' to include both 'complete' and 'partial' matches. So the number of partial matches will always be at least as high as the number of complete matches.

You should look at both results. If you don't have 248 core genes 'completely' present, the next thing is look at how many additional partial matches there are. If you have a result like 200/240 (i.e. 200 complete CEGs and 40 additional partial matches) then this at least suggests that most of the core gene set is present in your assembly, but some may be split across contigs or missing from the assembly. Remember, CEGMA only looks for genes that are located inside individual contigs or scaffolds. Theoretically, you could have an assembly that splits every gene across contigs which might lead to a 'complete' result of zero, and a partial result of '248'.

From looking at results of many different runs of CEGMA, it is common to see something like 90–95% of core gene present in the 'complete' category, and another 1–5% present as partial genes (for good assemblies at least). I have also seen one case where the results were 157/223. This is more unusual, suggesting that a relatively large number (27%) of the core genes were present as fragments. This might simply reflect lots of short contigs/scaffolds in the assembly. In contrast to this, one of the best results that I have seen is 245/248. It is rare to see all core genes present, even when you allow for partial matches.

Below is a chart that shows the results from 50 runs of CEGMA against different assemblies. The x-axis shows the percentage of 248 CEGs that were completely present, and the y-axis shows the percentage of CEGs that were only partially present.