Can AssemblyMapper keep contigs which are not mapped to pseudomolecules, like ragtag does?

aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

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Can AssemblyMapper keep contigs which are not mapped to pseudomolecules, like ragtag does? #41

Closed yaoxkkkkk closed 1 month ago

yaoxkkkkk commented 1 month ago

Thank you for you development. I just want to keep all contigs not only chromosomes, ragtag could keep unmapped contigs and can organise them to chr00. I wonder whether quarTeT had similar function?

Echoring commented 1 month ago

This is added in just released V1.2.2. With new option '--keep', the unplaced contigs will also be included in the draft genome. (not merged as chr00 though)

yaoxkkkkk commented 1 month ago

Thank you for your very soon update.