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runCA unitigger=bogart merSize=14 ovlMinLen= <ovl value> utgErrorRate=0.015 utgGraphErrorRate=0.015 utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm viaMiseq.frg |
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runCA unitigger=bogart merSize=14 ovlMinLen= <ovl value> utgErrorRate=0.015 utgGraphErrorRate=0.015 utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm viaMiseq.frg |
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The <ovl value> parameter was set to approximately 40% of your average corrected sequence lengths ([http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA ref]). ''As a general rule, if the average corrected length is less than 2.5Kbp, set it to 1000, if it is less than 3Kbp, set it to 1500, if it is less than 5.5Kbp, set it to 2000, if it is greater than 5.5Kbp, set it to 2500, and if it is greater than 6.5Kbp, set it to 3000.''
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