Performs viral de novo assembly on metagenomic reads against a large range of possible reference genomes. Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads. Scaffold de novo contigs against a set of possible references and subsequently polish with reads. This workflow accepts a very large set of input reference genomes. It will subset the reference genomes to those with ANI hits to the provid
This is a companion discussion topic for the original entry at github.com/broadinstitute/viral-pipelines/assemble_denovo_metagenomic