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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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Should the assembly be a reference genome? #181

Open elcortegano opened 2 years ago

elcortegano commented 2 years ago

Hi, I'd like to use circlator to assembly a mitochondrion genome. I have (PacBio) reads and "linear" contig-level assemblies for a number of samples, as well as a different "reference" chromosome-level assembly that includes the mitochondrion.

I am not sure how the assembly input files is used in circlator, so not sure either whether that input file should be the "reference" mitochondrion (i.e. the the same for all my samples), or a sample-specific whole-genome assembly . The objective is to detect variation between the mitochondrion assemblies.

Appart from the mitochondrion, would circlator be able to assembly any other extra-chromosomal circular DNA?

Thanks

phnghia99 commented 1 year ago

I have the same question, I have multiple "reference" mitogenomes and mitochondrion core genes. What exactly assembly.fasta input be? And what alternative it should be?