nsmt89

Thanks for the reply. I used different contig file as seed and it managed to produce a circularized assembly. However, I suspect the genome is still not complete. Even for...

Thank you for your suggestion. The output produced 4 smaller contigs after I changed the genome range. What do you think the reason? [log_Cryptocoryne_nurii6.txt](https://github.com/ndierckx/NOVOPlasty/files/4136722/log_Cryptocoryne_nurii6.txt) [log_extended_Cryptocoryne_nurii6.txt](https://github.com/ndierckx/NOVOPlasty/files/4136723/log_extended_Cryptocoryne_nurii6.txt)

Yes. Actually I use the largest contig from Fast-Plast assembly. If I did not invoke the extend seed function, the output will only be uncircularized genome. I will try the...

I just tried the version you gave me and its still produce the same result.

Yes but it will only produce small contig. [log_Cryptocoryne_nurii15.txt](https://github.com/ndierckx/NOVOPlasty/files/4150750/log_Cryptocoryne_nurii15.txt) [log_extended_Cryptocoryne_nurii15.txt](https://github.com/ndierckx/NOVOPlasty/files/4150752/log_extended_Cryptocoryne_nurii15.txt)

> > > But then you need to switch off extend seed directly, this option should only be used to extend an existing assembly... So could you try again without...

I tried your latest version of NOVOPlasty and it managed to output ~160kbp length size contig. How can I merge those contigs or see if I can get them circularized?...

My data is WGS. Attached is my extended log [log_extended_Cryptocoryne_nurii16.txt](https://github.com/ndierckx/NOVOPlasty/files/4162735/log_extended_Cryptocoryne_nurii16.txt) [log_extended_Cryptocoryne_nurii6.txt](https://github.com/ndierckx/NOVOPlasty/files/4162736/log_extended_Cryptocoryne_nurii6.txt)

Thank you for your time. I tried run with the seed you provided. Attached is my extended log: [log_extended_Cryptocoryne_nurii25.txt](https://github.com/ndierckx/NOVOPlasty/files/4183848/log_extended_Cryptocoryne_nurii25.txt)

[log_extended_Cryptocoryne_nurii18.txt](https://github.com/ndierckx/NOVOPlasty/files/4190286/log_extended_Cryptocoryne_nurii18.txt) Attached is the extended log. The reference is not really close but it is the closest that available currently; the same Family but different Order in taxa. I suspected...