Hello. I am looking for benchmark papers assessing the best reference guided transcriptome assembler using RNA-Seq data (which includes an assessment of StringTie). Any guidance would be greatly appreciated.
As always, no assembler could be universally considered better than another. I'd suggest Stringtie and Scallop2 (https://www.nature.com/articles/s43588-022-00216-1): the first for specificity (with a bit of parameters tuning) and the latter for sensitivity. Keep in mind that this comes from my personal experience with both, as respective authors claim for better performances and no recent extensive benchmark exists in literature.