We’ve added support for use of a reference sequence with DISCOVAR de novo. If you provide a reference sequence, then your assembly will be created de novo, then aligned to the reference sequence. Then when you view the assembly using
NhoodInfo, the view will be marked to show reference coordinates.
To use this new feature, supply the command-line option
REFHEAD=g, where you have files
g.names. The file
g.names should be a text file having the same number of lines as
g.fasta has records, with each line being a name for the corresponding record (e.g. chr3). These names are displayed by
NhoodInfo, so you want them to be reasonably short to avoid crowding the display.