How do the results above help me choose the best tool for my data and objectives?

[Juke34]

No description provided.

[Juke34]

I don't go into detail about the selection criteria for choosing the best tool, as this depends on the underlying biological issues, but I do calculate general statistics with FastQC. You should use the --fastqc to generate statistics.
I added a section in the README to go more into detail about what QC is available and where to find them.
I guess when I will add the description of how the outputs are structured (#19), this will become also clearer.

Is it enough to answer your concerns @rcannood ?

[Juke34]

I have now also added samtools stats to provide more comprehensive statistics. Everything is collected into a single report with MultiQC that can help to compare the aligners.
I do not want to go into details on which statistics to focus on to select an aligner. It depends a lot on the downstream task.
I have added a sentence in the manuscript to tell what statistics is available :

To facilitate aligner comparison, AliNe provides a comprehensive set of metrics, including computational resource usage (CPU, memory, runtime, and disk I/O) reported by Nextflow, as well as alignment statistics generated by FastQC [@fastqc] and Samtools stats [@samtools].

I hope these changes address your concerns.

[rcannood]

Thanks @Juke34 ! The information in the readme helps with being able to interpret the results :) Feel free to close this issue!