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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Assembly size is bigger than estimated size by genome survey #126

Open kuangtianhui opened 2 years ago

kuangtianhui commented 2 years ago

Dear Author,

When performing genome survey via Illumina pair-end data, it showed that the genome size is 9, 700 or 1,400 Mb. However, when I assembled my Nanopore reads using Nextdenove with genome size of ~9, 700 or ~1, 400 Mb, respectively. I found that the output of Nextdenove is ~2,100 Mb. So, my issue is why I get results with genome size bigger than genome survey?

Best wishes, Tian-hui Kuang

My version is the latest version.

moold commented 2 years ago

May be caused by duplicated assembly in heterozygous regions or multiple haplotype assembly for polyploidy genomes.

kuangtianhui commented 2 years ago

Thanks! I get rid of redundancy using purge_haplotigs_multiBAM, but only about 70 Mb were removed! There are any other ways commanded to solve this issue? Thank you again!

moold commented 2 years ago

It is hard to say. How about the assembly size by other assemblers?