README.md suggestion

[peterdfields]

Hi @ktrappe

I don't think the present samtools (v. > 1.x) will work with the present scripts. More recent versions of samtools require specification of the output file name when performing sort functions, and so an error arises in your present scripts. You might specific the samtools version requirement or update the script to use more recent samtools versions. A threading option on this step would also be great!

[ktrappe]

Thanks for the suggestion @peterdfields . We will try to incorporate a workaround for different samtools versions in our refactored version and look into the threading option (@eseiler )

[ktrappe]

Hi @peterdfields
A refactored and newer version of Daisy is available under https://gitlab.com/rki_bioinformatics/ in the DaisySuite project. DaisySuite includes Daisy and a novel tool, called DaisyGPS, that tackles the problem of finding suitable acceptor and donor references for Daisy. We reimplemented Daisy with the Snakemake framework that supports threading. DaisySuite is also available as a Conda package with all required tools and packages and now hopefully easier to install and more robust to use. Any feedback is welcome!