Hello, I am using spades for de novo assembly. How can I decide the kmer on the basis of sequence length? in my case sequence length is 125. Should I give this command? Pl, let me know.
spades.py -t 30 -k 21,33,55,77 --careful --only-assembler -1 E1_1.fastq -2 E1_2.fastq -o /SPADES_OUT1/ER_S6
You really don't need to decide that. By default that setting is set to auto and the program is going to pick the right parameters after analyzing the data.
I caution you against the --careful, at least until you assemble once without it. It will take longer to assemble with it, and the assembly may not be better. I also suggest not to use the --only-assembler unless you have error-corrected the data already. That switch would make the program run faster, but in my experience it is worth letting the program perform error-correction, especially when you have a metagenomic sample or very deep sequencing coverage. Once you error-correct the data it will be saved as such in your output folder. You can use those corrected reads if you assemble multiple times, and those subsequent runs you can go with the --only-assembler switch.
In short, I suggest that with each dataset you go first with the simplest set of switches (input, output and # of threads), and leave the other options for subsequent runs if needed.
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Thank you so much for the explanation sir. now I am using this command for WGS data of bitter melon.
spades.py -t 30 -1 E1_1.fastq -2 ER_2.fastq -o /SPADES_OUT1/ER_S6