Assembly size is smaller than estimated genome size

[nextomics]

Assembly size is smaller than estimated genome size

[moold]

Please change the value of seed_cutoff using bin/seq_stat. Do not use the default value of this option. After that, you can try this option: random_round = 100 and you will get a total of 100 results with 100 random parameter sets. But please check the accuracy of the assembly result using random parameters, which usually have more errors than the default result.
BTW, Could you use ENGLISH to ask help, which can provide some help to researchers in other countries.

[fengyuanli304]

Hi, Dr. Hu，I assemble the genome using NextDenovo2.3.1 and get a smaller genome size. We estimated the genome to be 544 Mb using flow cytometry. Could I adjust seed_cutoff using bin/seq_stat (from 30 to 44)?
seq_stat -g 520Mb -d 45

Type Length (bp) Count (#)
N10 18109579 2
N20 15369455 4
N30 14374265 6
N40 13453187 9
N50 10557259 12
N60 8958888 15
N70 7464108 19
N80 5225030 25
N90 1759737 36

Min. 38332 -
Max. 24878981 -
Ave. 3230002 -
Total 345610306 107
Thank you for your reading and I am looking forward to your reply.

[moold]

yes, and also see here