This program was created as a project assignment for Bioinformatics class at Faculty of Electrical Engineering and Computing, University of Zagreb.
SYNOPSIS
$ java -jar unitig.jar path_to_overlaps path_to_reads [-oLayout=outputLayout.afg] \
> [-oOverlaps=outputOverlaps.afg] [-epsilon=0.1] [-alpha=3]The program has 2 required and 4 optional arguments.
###Required:
-
path_to_overlaps - path to file containing overlap information
-
path_to_reads - path to file containing reads information
###Optional:
-
-oLayout - Specifies unitig layout file path in which the unitig layout will be written. If the file exists, it will be overwritten, if not, it will be created. If this argument is not provided, the unitig layout will be written to the standard output.
Use -oLayout=filepath to specify this argument -
-oOverlaps - Specifies unitig layout overlaps file path in which the overlap information from the unitig layout will be written. The same writing rules apply as in the unitig layout file path argument.
Use -oOverlaps=filepath to specify this argument -
ε - Real number value from [0,1] interval used in the transitive edge removal. Default is 0.1.
Use -epsilon=value to specify this argument -
α - Positive integer value constant used in the transitive edge removal. Default is 3.
Use -alpha=value to specify this argument
For additional reference about ε and α see this paper (pg. 13).
All optional argument names are case insensitive.
Use java -jar unitig.jar to run.
You can find example overlaps and reads files in the testData folder.
Valid example:
$ java -jar unitig.jar testData/overlaps.afg testData/reads.2k.10x.fasta -oLayout=outputLayout.afg \
> -oOverlaps=outputOverlaps.afg -epsilon=0.1 -alpha=3