Mikhail Kolmogorov

Hi, Flye applies additional coverage-based filtering to the final assembly, but not to the graph output. I think contig_3 was filtered out due to coverage. I can see that this...

Thanks for the info. In the "default" mode Flye is assuming uniform coverage distribution for all all sequences, but if you are interested in plasmid assembly I recommend using the...

Assuming that this has been answered - feel free to follow up if you have more questions.

Sorry for the late response! I think your method is fine. In general, for long unitigs / contigs you should get the same coverage / multiplicity values, compared to the...

Could you please send the full `flye.log` and tell a bit more about the machine (hardware, OS version etc)? Is the issue reproducible - e.g if you run Flye on...

Sounds good - note that `--asm-coverage` option only limits the memory usage of the first stage (disjointig assembly), since it's the main memory bottleneck. Polishing should not take a lot...

Hi Lily, Total length has reduced quite a bit - this is unexpected. I think it may have something to do with scaffolding. If you want to add additional polishing...