I would like to ask about the --genomesize parameter. Does it refer to the entire genome, including both the nuclear and organellar genomes?
Additionally, when I run PMAT with the script
PMAT autoMito -i Ccarlesii_ONT_dx1_dx0_1kb_q10.fastq.gz -o ./output -st ont -g 1G -tp all -tk all -cpu 40 -cs nextDenovo -np nextDenovo -cp canu -cfg Ccarlesii_ONT_1gb_Nextdenovo.cfg -m
NextDenovo starts running. Is NextDenovo assembling the nuclear genome?
I have previously used NextDenovo to assemble the nuclear genome. Is there a way to use the intermediate files from my previous nuclear assembly to facilitate the assembly of the organellar genome using PMAT?
Thank you for the help.
I would like to ask about the --genomesize parameter. Does it refer to the entire genome, including both the nuclear and organellar genomes?
Additionally, when I run PMAT with the script
PMAT autoMito -i Ccarlesii_ONT_dx1_dx0_1kb_q10.fastq.gz -o ./output -st ont -g 1G -tp all -tk all -cpu 40 -cs nextDenovo -np nextDenovo -cp canu -cfg Ccarlesii_ONT_1gb_Nextdenovo.cfg -mNextDenovo starts running. Is NextDenovo assembling the nuclear genome?
I have previously used NextDenovo to assemble the nuclear genome. Is there a way to use the intermediate files from my previous nuclear assembly to facilitate the assembly of the organellar genome using PMAT?
Thank you for the help.