Whole genome sequencing

I have forward and reverse FASTQ files from Whole genome sequencing. Could I use Qiime in the analysis of such data?
Or the Qiime is only for 16 srRNA.

Thank you.

Hi @zeineldn! QIIME 2 does not currently support the “upstream” analyses you’d use to process your WGS data. However, if you can generate a .biom file (i.e. feature table) from your data, you can import the feature table and continue “downstream” analyses that operate on feature tables as usual (e.g. alpha/beta diversity, ordination, etc).

QIIME 2 development has initially focused on marker-gene surveys, but we will be including more complete support for WGS, metagenomes, etc. in the future. I want to emphasize that QIIME 2 is not just a 16S rRNA analysis pipeline (this was a common misconception with QIIME 1). We currently support analyses of other marker genes, e.g. ITS and 18S. In fact, you can use any reference database that meets the formatting requirements expected by QIIME 2, so it’s not even limited to 16S, 18S, and ITS (we just provide out-of-the-box compatibility with the Greengenes, SILVA, and UNITE databases for convenience).

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