A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing

Recently, Booeshaghi and Pachter ([1][1]) published a benchmark comparing the kallisto-bustools pipeline ([2][2]) for single-cell data pre-processing to the alevin-fry pipeline ([3][3]). Their benchmarking adopted drastically dissimilar configurations for these two tools, and overlooked the time- and space-frugal configurations of alevin-fry previously benchmarked by Sarkar et al. ([3][3]). In this manuscript, we provide a small set of modifications to the benchmarking scripts of Booeshaghi and Pachter that are necessary to perform a like-for-like comparison between kallisto-bustools and alevin-fry. We also address some misuses of the alevin-fry commands and include important data on the exact reference transcriptomes used for processing[1][4]. Using the same benchmarking scripts of Booeshaghi and Pachter ([1][1]), we demonstrate that, when configured to match the computational com-plexity of kallisto-bustools as closely as possible, alevin-fry processes data faster (~2.08 times as fast on average) and uses less peak memory (~ 0.34 times as much on average) compared to kallisto-bustools, while producing results that are similar when assessed in the manner done by Booeshaghi and Pachter ([1][1]). This is a notable inversion of the performance characteristics presented in the previous benchmark. ### Competing Interest Statement Rob Patro is a co-founder of Ocean Genomics, Inc. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #fn-1