Description
- run metaphlan on all data
https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4
with this:
If you want to estimate the unknown fraction of a metagenome and your input file is a SAM file, remember to specify the metagenome size using --nreads. You can get easily get the metagenome size from a SAM file if you have run bowtie2 without the --no-unal parameter
- merge output files to a single file
https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#merging-tables
- view results
https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#heatmap-visualization
- calculate diversity
https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#alpha-and-beta-diversity-calculation
#!/bin/bash
#SBATCH --account=torch_pr_169_general
#SBATCH --job-name=metaphlan
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --time=16:00:00
#SBATCH --output=metaphlan_%j.log
#SBATCH --error=metaphlan_%j.err
wrappers started by NYU HPC team:
(I downloaded databases on my scratch)