Open Hans-zhao831 opened 3 years ago
Thanks for your feedback!
seed_cutoff
, and the -d
in seq_stat can usually be set to 30-45
, so you need to try different values, and I don’t have a better suggestion, if I have a better value, I will set it as the default.read_cutoff
or seed_cutoff
, you need to run it from beginning to end. If you change nextgraph_options
, just run the main task again, NextDenovo will rerun the assembly step only.Thanks for your reply.
Based on your experience, could you please provide a strategy for finding these optimal values (seed_cutoff and read_cutoff). For example,
Hi, Dr. Hu, thanks for developing such a powerful genome assembly software. Over the past half month, I've found that NextDenovo is the best in assembling the plant species I studied. The result made me so happy. But considering I haven't much experience in using the software, I'm still trying to obtain the best assembly results by adjusting the parameters, and in the process I have encountered some problems, so I would like to ask you for advice.
Before the consultation, I'll give you a quick overview of the project: PacBio data, ~110x raw data, diploid plants, 2g of genome size, 0.7% of heterozygosity, ~60% of repeat sequences, and nextDenovo v2.4.0.
1. How to detect the best parameters of read_cutoff and seed_cutoff, and their combinations ?
I obtained 4 versions based on different seed_cutoff and rest same parameters (read_cutoff=10k).
I also obtained 2 versions based on the two read_cutoff and rest same parameter (seed_cutoff=20k).
run2.cfg
Based on the above results, I confirm that seed-cutoff and read-cutoff have a big impact on the final assemble quality. However, I confused how to find the best value for each and the best combination of the two?
2. How can quickly obtain the final result after a few parameter changes without running from beginning to end.
Currently, I have to re-run the software from beginning to end after each parameter change, which takes a long time. Is there a way to quickly get the final result by modifying only one or a few parameters?
I look forward to your suggestions, and please don't hesitate to let me know if you need additional information.