View source for Bambus/printScaff

The '''printScaff''' command is a part of the [[Bambus]] pipeline.

PrintScaff requires as inputs the [[Bambus Manual#.evidence.xml|.evidence.xml]] file, the [[Bambus Manual#.out.xml|.out.xml]] file and the [[Bambus Manual#.lib file|.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 Manual|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 [[Bambus Manual#.oo file|.oo]] file listing all the contigs in each scaffold
* -sum - produce a [[Bambus Manual#.sum file|.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 [[Bambus Manual#Untangling scaffolds|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