tanaes / snake_strainer

Snakemake workflow for running inStrain on metagenomes

snake_strainer

Snakemake workflow for running inStrain on metagenomes

Steps

Dereplication

• import genome list
• download genome file
• run drep
• create scaffold to bin
• run Prodigal

Read mapping

• index drepped genome list
• map reads

inStrain

• profile
• compare