ViReMa Files

Updates to ViReMa version 0.5

Output Files are generated as needed, rather than are the beginning of Compiler_Module.py.


Option:

--BED

"Output recombination data into BED files."

This option will output the Virus and Host Recombination results into an ouput files called Virus_Recombination_Results.bed, Virus_MicroRecombination_Results.bed, Host_Recombination_Results.bed and Host_MicroRecombination_Results.bed, within a subdirectory called BED_Files in the output_directory specified by the user.  These are BED6 files (with version 0.5.1) and so can be read into, for example, the Interactive Genome Viewer (IGV).  Only intra-gene recombination are compatible with this format (with version 0.5.1).  Inter-gene recombinations will be handled using alternative BED formats in a later version.  BED files have with 'graphType=junctions' in the track name and so can be displayed similarly to splice junctions.

Will also write out a BEDGraph file illustrating conservation over virus genome as demonstrated in Figure 4, Routh et al NAR 2014 Jan 42(2):e11