sometimes quick merge does not merge contigs? about quickmerge HOT 3 OPEN

On Thu, Oct 21, 2021 at 7:20 AM zzz ***@***.***> wrote: Dear developers, thanks a lot for writing this nice tool! I used the quickmerge frequently to merge my assemblies from PacBio and Nanopore. Most of the time I see a successful big improvement of NG values, but sometimes quickmerge doesn't seem to merge the query contigs, though no errors was reported and all files were generated. For example, I used Nanopore assembly (NG50 ~ 10M) as the reference to merge contigs from PacBio assemblies (NG50 ~ 4M). In the failed case, the resulted merged assembly has the same NG50 value (or only several k bp difference) and the same number of contigs as the query assembly, even if the parameter -l was set to the N50 value of the reference (Nanopore). In this case, if I lower the -l value significantly, say 2M, then the continuity of the resulted assembly is improved. But I'm kind of hesitated to use the merged ones generated with a lower -l value... I had merged around 8 genomes, among which I had three failed cases. I don't know where could be the problem, as the contigs seem aligned well between nanopore and PacBio assemblies, when I aligned them by mummer outside of quickmerge. Could you please give me some hints where the problem could be? Or how should I deal with this problem? Thanks a lot in advance! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#67>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2G2HJAF2KYPNBMXCO3UIAOJJANCNFSM5GOIOXCQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.