RegapLite

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RegapLite
Function Gap handling
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, OUTDIR, GDB, NO_HEADER
Special CLAs SUPER_ID, WRITE, MERGE, AGGRESSIVE, FIND_GAPS, USE_SHORT_LINKS_ONLY, TRIM_UNMERGEABLE_PAIRS, MAX_SCORE, SHORT_LINK_MAX_SEP, MAX_DISCREPANCY
Source location ARACHNE_DIR/assemble_alt

RegapLite is an assembly module that fixes the layout of supercontigs. It checks the supercontigs in an assembly for obvious misassemblies, such as negative-sized gaps that can be eliminated by connecting the surrounding contigs. RegapLite should be run with WRITE=True in order to write to the OUTDIR. In script modules, it is often run immediately preceding or succeeding CloseGaps (which performs a similar function) or Rebuilder.

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