Comparison of RNA velocity methods for droplet scRNA-seq data

Method ID	Agreement	Strand-aware	Counting of multi-gene reads	Comments
alevin_sep_gtr	good	yes	yes
alevin_coll_gtr	good	yes	yes
kallisto|bus_sep_excl	good	no	no	Reads in ambiguous regions typically discarded
starsolo	good	yes	no
alevin_coll_decoy_gtr	variable	yes	yes
velocyto	variable	yes	no
kallisto|bus_coll_excl	variable	no	no
alevin_sep_decoy_gtr	poor	yes	yes	Reads in ambiguous regions double-counted.
alevin_spliced_unspliced_gtr	variable	yes	yes	3’ tag protocols does not provide enough information for spliced/unspliced resolution.
dropest	poor	no	partially	Insufficient UMI collapsing
kallisto|bus_coll_incl	poor	no	no
kallisto|bus_sep_incl	poor	no	no	Reads in ambiguous regions double-counted.
starsolo_diff	variable	yes	partially	Non-zero unspliced count possible even without introns; nominally negative unspliced count possible.

Reference: Soneson C, Srivastava A, Patro R, Stadler MB. Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS Comput Biol. 2021 Jan 11;17(1):e1008585. doi: 10.1371/journal.pcbi.1008585. PMID: 33428615; PMCID: PMC7822509.