Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

SOAPdenovo parameter -K #89

Open
17863952296 opened this issue May 10, 2023 · 0 comments
Open

SOAPdenovo parameter -K #89

17863952296 opened this issue May 10, 2023 · 0 comments

Comments

@17863952296
Copy link

Hi, I try many different parameter K while using SOAPdenovo to assemble Streptomyces spp. genomes( 7-10M), but good results were still not got. The size of the genome in the result file(*.scafSeq) is about 2.8M at most. So now I don't know how to solve this problem?
Here is the configuration file I set up and the command to run it:
config.txt:
max_rd_len=150
[LIB]
avg_ins=409
reverse_seq=0
asm_flags=3
rd_len_cutoff=150
rank=1
pair_num_cutoff=3
map_len=32
q1=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R1.fq.gz
q2=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R2.fq.gz
run the command:
/usr/local/SOAPdenovo2/SOAPdenovo-63mer all -s CYX02C3D3.config.txt -K 45 -p 16 -R -o CYX02C3D3/result
Of course, I tried other values of K(23, 31, 35, 63......), but it didn't work.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant