CloseGaps

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For the module that uses read trimming, see UntrimToCloseGap.
CloseGaps
Function Gap handling
Phase Assembly
Standard CLAs PRE, DATA, RUN, OUTDIR, GDB, NO_HEADER
Special CLAs INDIR, WRITE, VERBOSE, TEST_BLESS, AGGRESSIVE, FILTER_AGGRESSIVE, SUPERS, OVER_EXTRA, DEV_EXTRA, K, MAX_DEV, MIN_OVERLAP, LOCAL_ALIGN
Source location ARACHNE_DIR/assemble_alt

CloseGaps is an assembly module that merges consecutive contigs within a supercontig, thus closing the gap between them. It is often run before or after RegapLite, which performs a similar function.

The CloseGaps algorithm is as follows: Loop over every pair of consecutive contigs in every supercontig. For each pair of contigs, attempt to find an alignment between them; if an alignment is found, use it to merge the contigs. The methods of finding an alignment are, in order:

  • Look for an alignment using AlignTwoBasevectors.
  • Look for a shared mutmer with length ≥ 80 bp, error rate ≤ 3%, and pairing distortion ≤ 4 sd.
  • Look for a shared mutmer with length ≥ 200 bp, error rate ≤ 1.5%, and pairing distortion ≤ 2 sd.
  • Look for a shared sequence of C's or G's of length ≥ 14, with pairing distortion ≤ 2 sd.
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