How to Run Verkko Consensus Using a Fixed Path#
After fixing the paths and filling the gaps with new paths, you can run Verkko consensus using the updated path file based on the original Verkko assembly directory. The vf.pp.mkCNSdir(obj, new_folder_path) function uses obj.verkkoDir as the base directory and copies the necessary files and folders to new_folder_path. The final fixed path (GAF) will be saved in new_folder_path/6-layoutContigs/consensus_paths.txt. It is always a good idea to check whether the final path file contains the gap-filled paths. Please confirm this before running Verkko consensus. You can then run the Verkko consensus command as shown below:
baseDir=base_folder_path # output of original Verkko assembly
outDir=new_folder_path
path="outDir/6-layoutContigs/consensus_paths.txt" # This should contain the final paths, including the gap-filled paths.
hifi="/path/to/hifi1.fastq /path/to/hifi2.fastq " # Provide a space-separated list of HiFi read file paths
nano="/path/to/nanopore_reads1.fastq /path/to/nanopore_reads2.fastq"
verkko \
--snakeopts "--dry-run" \
--slurm -d $outDir \
--hifi $hifi --nano $nano \ # Since Verkko 2.3, it is no longer necessary to include the --hifi and --ont parameters, as they are automatically detected and used within Verkko.
--paths $path --assembly $baseDir
The --dry-run option in Verkko will simulate the steps to be executed with the newly generated directory. Ensure that the layoutContigs step is included in the list of steps to be executed. Below is an example of the expected job statistics for a Verkko consensus run:
Job stats:
job count min threads max threads
---------------- ------- ------------- -------------
buildPackages 1 8 8
cnspath 1 1 1
combineConsensus 1 8 8
layoutContigs 1 1 1
total 4 1 8
Once verified, you can proceed with the actual run by removing the --dry-run option, as shown below:
verkko \
--slurm -d $outDir \
--hifi $hifi --nano $nano \
--paths $path --assembly $baseDir