Basic Usage
MetaGEAR requires 3 databases: Kneaddata, MetaPhlAn, HUMAnN. These can be downloaded by running the command:
metagear download_databases
To run the QC and Microbial Profiles workflows, run:
metagear qc_dna --input samples.csv
metagear microbial_profiles --input samples.csv
metagear qc_dna --input samples.csv -preview # generate script only
The output directory defaults to ./results when --outdir is not specified.
Preview mode:
Running with -preview prints the generated script instead of executing it.
For instance, when running
metagear qc_dna --input samples.csv -preview
The file metagear_qc_dna.sh is generated in the current directory and can
be executed manually, or the command can be re-run without -preview to directly run the pipeline.
Input format
The input file should look like this:
sample,fastq_1,fastq_2
SAMPLE-01,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz
SAMPLE-02,/path/to/sample2_R1.fastq.gz,/path/to/sample2_R2.fastq.gz