I got a little confused with the version of KneadData. I installed the KneadData by “git clone” + “python setup.py install” commands. The “pip list” command showed that I have kneaddata 0.11.0 but kneaddata --version command still shows 0.10.0. The tag at the github page also shows 0.10.0 as the latest. I appreciate if this descrepancy could be solved.
The tutorial page looks like based on version 0.11.0, but the one installed via downloaded tar.gz was 0.10.0. This old version cannot use --input1 and --input2 options, which is used in the tutorial, and could be a source of confusion for paired-end read users. I found that 0.11.0 solved some problems for operating paired-end reads, so I hope it reaches users more easily.
My apologies if you are already working for it. Anyway, thank you so much for developping this great tool!