VerifyAssemblyIntegrity is a module that performs simple tests on a completed draft assembly and determines whether anything is seriously wrong with it. The tests include, in accordance with the ValidateAssembly module:
- Check for contigs of length zero and contigs with different number of bases and quals.
- Check supers for absurdly large gaps (|gap size| > 1000000).
- Check for supers with no contigs.
- Check for contigs that do not appear exactly once in the supercontigs.
- Check for read locations out of order.
- Check that read locations have correct read (if CHECK_READ_LENGTH = True) and contig lengths in them.
- Check for zero-length reads in contigs.
- Check for contigs having no reads.
- Check that no contig contains the same read twice.
- Check for read which extend more than 5kb off the end of their contig.