Contig QC with QUAST in qiime2 MOSHPIT

Technical Support
1

Hi.

I used qiime2 MOSHPIT, following the tutorial.

at a point when I am doing Contig QC with QUAST it giving the following error: (1/3) Missing option '--o-results-table'. ("--output-dir" may also be used)
(2/3) Missing option '--o-reference-genomes'. ("--output-dir" may also be
used)
I am asking what to put for --o-reference genome becouse this this untargeted metagenoics, so no particuler genome we can put as refference.

what command can I used to run QUAST without the reference genome?

2

Hello @Nondumiso_L_Ntuli,

The --o-reference-genomes, according to the command line help text, are either:

  • the reference sequences that the QUAST software downloads if you don't provide an input to --i-references, or
  • the reference sequences you provided to --i-references

So in your case it sounds like it would be the former. I'm not very familiar with QUAST but I believe what is happening is that it queries some database with each contig, downloads a reference genome that the database considers the best match, and then aligns one or more contigs to the reference genome. Hopefully this clears up the confusion.

3

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