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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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Flye output only 1 contig #675

Closed LaurenBaena closed 3 months ago

LaurenBaena commented 4 months ago

I'm assembling a ~5 Mb bacterial genome using ONT reads. I should have very high coverage based on pre-assembly calculations (~1400x), so I used the modifiers, --genome-size 5m --asm-coverage 50, as suggested in another thread about no disjointigs assembled. This finally let my assembly complete, but it produced only 1 contig for the output. The length is in the target range, but every tutorial and example I've seen with flye produces multiple contigs. This also produces weird comparisons to my reference genome when I run QUAST because of the single contig. Is a single contig in itself a bag thing? Could this be because of the high mean coverage (which my flye log puts at 1175x)?

I'm attaching my flye log to this issue. Any insight is appreciated!

Thank you, Lauren flye.log

mikolmogorov commented 4 months ago

Hi Lauren,

This happens fairly often with bacterial genomes, this likely means that your assembly is complete.

Misha

mikolmogorov commented 3 months ago

Assuming this has been answered, feel free to follow up if you have more questions!