About Centrifuge and Centrifuger's running commands: the read files for the -2 option
Thank you for conducting this comprehensive and marvelous benchmark study. It is also remarkable that you already incorporate Centrifuger into the benchmarks. When I explored the results, I found Centrifuge and Centrifuger's results seems lower than other tools by a margin more than what I expect. Therefore, I looked in the running commands and noticed that https://gitlab.com/ezlab/lemmi-v2/-/blame/v2.2.0/resources/candidate_containers/centrifuger_100/LEMMI_analysis.sh#L14 put read1 as the input file for -2, which should be the file for read2. This issue also happens in Centrifuge: https://gitlab.com/ezlab/lemmi-v2/-/blame/v2.2.0/resources/candidate_containers/centrifuger_100/LEMMI_analysis.sh#L14 . Did I look at the wrong files or these are indeed typos? Thank you!