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Table 6 Exonerate (v.2.2.0) parameters used for mapping de novo contigs back to the reference genome

From: Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

Parameter Value Parameter Value
model affine:local gappedextension FALSE
bestn 50; 100 for inversions joinrangeext 300
gapexend -3 score 15
dnahspdropoff 10 dna submatrix values (inversions) 5 for match, -15 for mismatch
hspfilter 200