Assembly size is smaller than estimated genome size

Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

GNU General Public License v3.0

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Assembly size is smaller than estimated genome size #14

Closed yilunhuangyue closed 4 years ago

yilunhuangyue commented 4 years ago

你好，在软件释放后立即初步体验了一下。使用的基因组预测大小为320M，杂合度为0.7%。最终N50达到了11M，基本达到了染色体水平，对这个水平非常惊喜。很感谢能开发出这样的软件。但有一个问题，目前组装的基因组大小为273M，使用数据为nanopore raw data，参数均为默认。与其他软件相比（wtdbg2:293M，minimap+minisam：321M，SMARTdenovo：297M），还有一定差距，请问调节什么参数可以适当增大组装的基因组大小呢？期待开发者的解答。后续也会继续使用反馈。再次感谢开发者做出的贡献~

moold commented 4 years ago

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 commented 2 years ago

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 commented 2 years ago

yes, and also see here