Skip creating combined reference for metaQUAST about quast HOT 2 OPEN

Hi!

Am I correct that you want to specify a single MULTI-FASTA file as reference and than get metaQUAST output as if it was supplied by multiple SINGLE-FASTA files? I.e. get separate reports ("per-reference" runs) for each entry in your reference.

Currently you can specify a single file with -R flag but metaQUAST will not split it, so you would get only two reports: for the combined reference and for one "per-reference" run (which will be similar because the combined reference would be equal to your reference). We do not split MULTI-FASTA reference files because usually such a reference contains several chromosomes (or a chromosome plus several plasmids) of a single genome, so splitting it into separate FASTA-entries looks incorrectly.

However, if you find this useful, we can add an additional flag for forcing metaQUAST to split input files into SINGLE-FASTA entries and process them as independent references.

from quast.

My hope was to be able to specify both the separate SINGLE-FASTA files and the concatenated MULTI-FASTA file in order to skip the file concatenation step to hopefully take some run time off of QUAST as I am using multiple times.

I can just specify multiple SINGLE-FASTA files and get the same results, so if it is hard to do what I am asking, I can just do that :)

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