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Would circulator change the assembly? #189

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isabelluo opened this issue Jul 19, 2024 · 0 comments
Open

Would circulator change the assembly? #189

isabelluo opened this issue Jul 19, 2024 · 0 comments

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@isabelluo
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I have a genome assembly that was assembled carefully with Trycycler that was only one contig and yet uncircularized. Trying to circularize it with circlator, and annotating it and I found the result slightly changed.

Pre-circularization:
Genome length 2948785
CDs:2733
hypotheticals:141

Post-circularization:
Genome length 2948782
CDs:2732
hypotheticals:142

The following is my command:
circlator all --merge_min_id 85 --merge_breaklen 1000 --threads 10 cas_124370.fasta cas124370.fastq cir_cas_124370

Why is there a subtle change on this? should I be concerned about the change on the assembly? I hope the slight changes is only mergning the ends but not changing anything else, since I used a really robust pipeline to assemble the genome using Trycycler and trust it more.

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