The functionality of Consed will be greater if the .scf and .phd files which PHRED produces are also available. The ace files created by Arachne have only been tested with consed releases 7.52 and 12.
|Argument name||Argument type||Default value||Meaning|
|ACEDIR||String||[None]||The directory in which the ace files and CreateAceFile.log are created. A subdirectory of DATA.|
|explicit_acedir||String||[None]||An alternative to ACEDIR: the same directory, but specified in full, rather than relative to DATA.|
|Type||String||All|| Controls which supercontigs are written to the ace files.
|Index||Index list||[None]||Required if Type=Index, to specify supercontig ids. For example, if Index='[1-3,5]' then the command would produce four .ace files in ACEDIR: ace_file_name.1, ace_file_name.2, ace_file_name.3, and ace_file_name.5, corresponding to supercontigs 1, 2, 3, and 5.|
|TopN||Integer||0||Required if Type=Top.|
|Cutoff||Integer||1||An additional restriction (beyond Type) on chosen supercontigs. Supercontigs whose constituent contigs are all shorter than Cutoff are ignored.|
|ONE_FILE||Bool||True||If True, all chosen supercontigs are written to a single file, called supercontigs.ace. Otherwise, the chosen supercontigs are each given their own file, called supercontigs.ace.id, where id is the supercontig's id.|