Bambus/printScaff

The printScaff command is a part of the Bambus pipeline.

PrintScaff requires as inputs the .evidence.xml file, the .out.xml file and the .lib files produce by Bambus, the minimal invocation being:

printScaff -e test.evidence.xml -s test.out.xml -l test.lib

Optionally you may specify the output prefix with option -o (just like in the Bambus invocation). PrintScaff has parameters that control what gets reported, and in what format.

In the first category you have:

• -dot - produce a .dot file
• -detail - produce a .details file
• -oo - produce a .oo file listing all the contigs in each scaffold
• -sum - produce a .sum tab delimited list of scaffold stats (#contigs, size, and span)
• -f <fasta_file> - generate a pseudo-molecule for each scaffold using the contig sequences listed in <fasta_file>. Note that the contigs in the scaffold files are names "contig_<id>" while the contigs in the <fasta_file> must simply be called "<id>". Note that this option together with the default -merge option (see below) is meaningless unless you've untangled the scaffold.
• -phys - create a .phys file listing all "gaps" spanned only by the specified libraries:

printScaff -e test.evidence.xml -s test.out.xml -l test.lib -phys MUMmer

will generate a file called test.phys that contains all contig pairs linked by nothing but MUMmer links.

In the second category you have:

• -page - produce .dot file formatted for printing on 8.5x11" paper
• -plot - produce .dot file formatted for printing on a plotter (36x48" paper)
• -unused - draw edges corresponding to unused links
• -merge - (default) when the -f option is given, produce a pseudo-molecule for each scaffold by adding 60 N characters between the contigs in the scaffold
• -nomerge - when the -f option is given, create a fasta file containing all contigs in each scaffold in the correct orientation