Closed bensprung closed 1 year ago
NextDenovo
on a 32 GB RAM Computer, the RAM is too small.NextDenovo
.So, I suggest you can try with other assemblers.
OK. How much RAM is the minimum, for a 12 Mbp genome? (And I do have more ONT reads, I only gave it a subset to try it out. I think I have up to 800x coverage. Definitely 400x. )
FWIW I did get a reasonable-looking assembly out using these parameters:
[General]
job_type = local # local, slurm, sge, pbs, lsf
job_prefix = nextDenovo
task = all # all, correct, assemble
rewrite = yes # yes/no
deltmp = yes
parallel_jobs = 1 # number of tasks used to run in parallel
input_type = raw# raw, corrected
read_type = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = BGS1_uncorr_nextDenovo
[correct_option]
read_cutoff = 1k
genome_size = 12m # estimated genome size
sort_options = -m 8g -t 4
minimap2_options_raw = -t 4
correction_options = -p 1
[assemble_option]
minimap2_options_cns = -t 4
nextgraph_options = -a 1
Thanks. What do you mean by the top 60X longest? Select the longest reads sufficient to give 60X coverage?
Yes
Got it. Thank you.
Hi, I can't figure out how to set various parameters in a self-consistent way. I'm on a desktop with 6 cores, 32 GB RAM, working with a yeast genome of ~12 mb and about 230x coverage with ONT reads, so about 2.8e09 bases. The FAQ says:
Since
parallel_jobs
comes to32/64
, I assume I should set it to 1?pa_correction
comes to 32e09/(2.8e09*1.2/4) = 38. But thenP/pa_correction
= 6/38 << 1, so I'm not sure how to proceed.I also got the following warning:
I left
read_cutoff = 1k
and I setgenome_size = 12m.