Comments (3)
adigenova
commented on September 12, 2024
Hi,
Nice that the parameters help you to improve the assembly. Regarding the genome size, can you tell me which is the estimated (k-mer) and the genome size assembled by Wengan?.
thanks!
Best,
Alex
from wengan.
bioinformaticspcj
commented on September 12, 2024
Hi Alex,
I estimated the genome size by (17-mer), results show it is 1.62Gb. But, the wengan assembly is 1.56Gb.
Thanks.
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主题: Re: [adigenova/wengan] Why the assembly size is smaller than expected? (#44)
Hi,
Nice that the parameters help you to improve the assembly. Regarding the genome size, can you tell me which is the estimated (k-mer) and the genome size assembled by Wengan?.
thanks!
Best,
Alex
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adigenova
commented on September 12, 2024
Hi,
It seems that the difference in size is in the expected range (~60Mb). These should be sequences related to repeats, centromeres, or large segmental duplications that are still hard to assemble for most assemblers (including Wengan).
So, I do not have feedback to provide this time.
Best,
Alex
from wengan.
Related Issues (20)
- Error 139 HOT 4
- Setting new tmp directory for intermediate files HOT 1
- error2 HOT 3
- asm1.minia.41.contigs.fa] Error 127 HOT 3
- "--clib" flag error in intervalmiss HOT 2
- Using error corrected long reads HOT 2
- Error 137 HOT 4
- Is adapter filtering needed? HOT 1
- Unhandled kmer size HOT 1
- issues with non IUPAC bases HOT 1
- unrecognized command 'iupac2bases'. Abort! HOT 1
- Installatation HOT 1
- SPolished.asm.wengan.fasta] Error 136 HOT 3
- Leveraging ONT raw and PacBio raw HOT 1
- Error 132 - linger
- Wengan error 1 HOT 2
- Error 136
- make: *** [m013330.mk:4: m013330.abyss2-contigs.fa] Error 2 HOT 2
- Unable to install DiscovarDenovo
- Final assembly too small HOT 5
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