Generate two phased Juicebox .assembly files from one master .assembly for FALCON-Phase. After generating a set of scaffolds for a single phase (or a master consensus haploid scaffold) and exporting the results from Juicebox as a .assembly file, this tool will use that .assembly file plus phasing information from FALCON-Phase to produce a pair of true phased .assembly files describing each set of scaffolds.
usage: update_assembly.py [-h] -a File -p File
[--sequence-length SEQUENCE_LENGTH]
[-l {WARNING,INFO,DEBUG}]
Update Juicebox assembly file to use one haplotype
optional arguments:
-h, --help
show this help message and exit
-a File, --assembly File
Assembly file name
-p File, --phase File
FALCON-Phase output file name
--sequence-length SEQUENCE_LENGTH
Length of sequence names. Default is 9
-l {WARNING,INFO,DEBUG}, --logging {WARNING,INFO,DEBUG}
Logging level
The assembly file update_assembly.py expects is the single phase/master consensus haploid scaffold .assembly file from Juicebox.
The FALCON-Phase output file update_assembly.py expects is generated by the falcon-phase phase command in the FALCON-Phase package.