Documentation of output files

[Peter Cock]

The main README file appears to be the only documentation for running resfinder locally: https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md

This does not appear to describe the meaning of the assorted output files, nor how they match up to what is shown on the webserver which has some output documentation here: https://cge.cbs.dtu.dk/services/ResFinder/output.php

For example, having run with -c and -acq, I get the following output files and folders:

pheno_table_escherichia_coli.txt
pheno_table.txt
pointfinder_kma/
PointFinder_prediction.txt
PointFinder_results.txt
PointFinder_table.txt
ResFinder_Hit_in_genome_seq.fsa
resfinder_kma/
ResFinder_Resistance_gene_seq.fsa
ResFinder_results_table.txt
ResFinder_results_tab.txt
ResFinder_results.txt
std_format_under_development.json

What are they all?

Are the pheno_table*.txt files alternative representations of the ResFinder_results*.txt files (not using the PointFinder_*.txt information)?

[CGE Helpdesk]

Dear Peter,

Thank you for your interest in ResFinder and for making us aware of the the missing information on the output files.
A brief description for each file has been added to the README. I hope this will bring clarity into what the different files contain and answer your questions.

Best,
Karen, CGE Helpdesk

[Peter Cock]

Thank you Karen,

Those additions to the README in commit da7b9d8d03d2dc45af67028b3d59a094cbe3f518 cover the fundamentals concisely. I’m happy to mark this issue as resolved.

Peter