T2T assembly supporting tools

Question

[eva_u]

Hi all,

Has anyone used t2t assembly with transcriptome data? If yes, single cell RNAseq or bulk? Which aligner(s) did you use?

Thank you!

[biofalconch]

I think it is uncommon to use RNA-seq data for t2t assemblies as they usually are use for scaffolding rather than to fill gaps in a genome, but that aside, I wouldn't use single cell since it usually 3' biased, you would like to have a good coverage of the entire gene body to increase the chances to scaffold two contigs that span the same gene.