VerifyAssemblyIntegrity

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VerifyAssemblyIntegrity
Function Text output
Phase Analysis
Standard CLAs PRE, DATA, RUN, GDB, NO_HEADER
Special CLAs INDIR, CHECK_READ_LENGTH, MAX_ERRORS_TO_PRINT
Source location ARACHNE_DIR/assemble

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.
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