Improved docs on output files

[nick-youngblut]

I'm trying to get the locations of all genome locations where quast identifies a mis-assembly (not just summaries of # of mis-assemblies). I'm running metaquast (with genome references (the metagenomes are simulated from the genomes) and I'm providing the simulated paired-end HiSeq reads to metaquast for SV detection.

metaquast generates a lot of output files, an while there is a general description of many of them in the manual (Thanks!), many others are not really described (at least that I can find). For instance, the reads_stats/combined_reference.bed file is not described. For my test dataset, all values under the "TYPE" column are "QuastDEL". I'm guessing that "QuastDEL" refers to a deletion, but it would be good to confirm this. Also, what are the other possible "Quast*" values that could be in the *.bed file?

The contigs_reports/contigs_report_contigs.mis_contigs.info also seem useful for determining the locations of all mis-assemblies, but what is the structure of this file format? This info would be really helpful for parsing the file.

Are there any other output files that would be useful for determining the locations of mis-assemblies?

quast version: quast 5.0.2 py36pl526ha92aebf_0 bioconda