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Function File output
Phase Output
Special CLAs ACEDIR, explicit_acedir, AceFile, contig_naming, Index, Type, TopN, Cutoff, StartContig, StopContig, ONE_FILE, REMOVE_SCF, CLEAN, PRELOAD_READS, PRELOAD_CONTIGS, USE_FASTB
Source location ARACHNE_DIR/assemble

The CreateAceFile module writes ace files, which are used as inputs to Consed. CreateAceFile requires that FixLocations be run prior to it, in order to produce the file mergedcontigs.pma.

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.

Command-line arguments

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.
  • Type=All will create Ace files for all supercontigs.
  • Type=Index will use supercontigs whose ids are specified in Index.
  • Type=Top indicates that the TopN largest supercontigs should be chosen.
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, where id is the supercontig's id.
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