Github.com/broadinstitute/viral-pipelines/metagenomic_denovo

Assisted de novo viral genome assembly (SPAdes, scaffolding, and polishing) from metagenomic raw reads. Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2 and optionally using BWA, BLASTN, and/or BMTAGGER databases), and FASTQC/multiQC of reads.


This is a companion discussion topic for the original entry at github.com/broadinstitute/viral-pipelines/metagenomic_denovo