Mikhail Kolmogorov

@elcortegano with the latest code Flye should only use lower confidence alignment, if the coverage of "reliable" alignments (that is, non-secondary, non-supplementary, MAPQ>30) is low. Do you use MAPQ filter...

@elcortegano yes, according to documentation pbmm2 discards all supplementary alignments. I suggest doing the same analysis with minimap2 with `-ax map-pb -p 0.5 -z 1000`.

Well, I guess one last thing to check is if showing secondary (and supplementary) alignments is enabled in your IGV settings. Check both "alignment" and "third gen" tabs. It seems...

Hi Brian, Definitely looks like a Flye artifact. Currently, the algorithm does require support of multiple reads within the contig, but contig ends may be extended with a single longest...

I would also make sure that you are running the latest version of conda (`conda update -n base conda`). Also, try being explicit with the python version: `conda create -n...

@tujiaki please check my suggestions from the post above and post the full terminal output of each command in case they fail.

@HuoJnx what's the output of `conda create -n flye_29 flye=2.9` ?

@jjkoehorst @louellette try `conda create -n flye_29 -c bioconda flye=2.9`

Hi, Stretches of Ns represent unknown sequence. Ragout does not attempt to fill these gaps from reference sequences. It only orders/orients the input target sequences into scaffolds, but does not...

Hi, Looks like minimap_stderr log is from a different run (different file names). Could you submit the matching one?