ContigSanitizer

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ContigSanitizer
Function Cleanup
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER
Special CLAs CONTIG_IDS, END_FORGIVENESS, compute_gap_devs
Source location ARACHNE_DIR/assemble_alt

The module ContigSanitizer removes "bald spots", or regions of zero read coverage, from the contigs in an assembly. If a contig has an internal "bald spot", it will be split into smaller contigs. ContigSanitizer relies on the function ContigSanitize in the AssemblyOps module.

Because read-to-contig alignments are described by ReadLocation objects, any assembly module that modifies or removes ReadLocations may inadvertently create "bald spots". Such modules include VacuumLocs and FixLocations. In module pipelines, it is common to run ContigSanitizer shortly after running these modules.

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