HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Problem with de novo assembly of single circular contigs in Genomics Workbench 6.5.2, 7.0 and Assembly Cell 4.2.1

3.16. Problem with de novo assembly of single circular contigs in Genomics Workbench 6.5.2, 7.0 and Assembly Cell 4.2.1

A problem has been discovered in the Genomics Workbench versions 6.5.2 and 7.0, CLC Genomics Server 5.5.2 and 6.0, and the Assembly Cell 4.2.1. This problem will affect only a very tiny minority of cases.

This issue was fixed in the CLC Genomics Workbench 7.0.1, CLC Genomics Server 6.0.1 and Assembly Cell 4.2.2.

When does this problem arise?

Using the affected software versions, both the following need to be true for this problem to arise:

  • a complete, circular contig is output in the assembly results (i.e. a single contig, which is circular)
  • those who have assembled their data using one of the software versions listed above.

As assembling directly into a single contig is rare, this issue will likely arise very seldom in practice and would be expected to occur only in cases where the assembly involves a very small circular genome (e.g. a plasmid).

How can you tell if your assembly is affected?

There is currently no obvious reporting of when a contig has been detected as being circular by the assembler. In practice, this issue should only affect you if you working with data expected to assemble to a very small, circular contig, and only in those cases where it results in a single contig.

If this is true for your assembly, then when this issue arises, the symptom is that only the first part of the contig will be output correctly. The remaining part of the contig will either contains random nucleotides or it will not be output at all. For example, in the single case of this we have observed in practice, the contig in question contained over 97% A characters. How much of the contig the assembler is able to output correctly will vary, but in most cases the correct region will be about 100bp or less.

 

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