Parsable output please about checkm

[donovan-h-parks]

Just to follow-up. There is also a -f flag to write the table (and only the table) to file. CheckM produces many different outputs with the tree_qa and qa commands which can be run after the complete lineage or taxonomic workflow.

[ctSkennerton]

There is an option called --tab_table that will produce a tab separated table without the fancy formatting for easy parsing

[xapple]

OK, that's good. It should probably be the default ?

I have to admit, with bioinfomartic tools, it's often that you just try them out quickly, see if they are worth anything before integrating them to your workflow. You certainly don't have time to go through all the command line options of every tool you want to try.