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metAMOS is an integrated assembly and analysis pipeline for metagenomic data. It is built around the Bambus2 metagenomic scaffolder and includes many current tools for assembly, gene finding, and taxonomic classification.

How to Use

metAMOS uses environment modules. Type

module load metAMOS

at the prompt.

Interactive Use

module load metAMOS
initPipeline -f -m carsonella_pe_filt.fna -d test_bowtie2  -i 500:3500
runPipeline -a soap -m bowtie2 -c kraken -g fraggenescan -p 15 -d test_bowtie2 -k 25 -f Assemble,MapReads,FindORFS,FindScaffoldORFS,Abundance,Classify,Annotate -n FunctionalAnnotation


A typical slurm script would be as follows:

# This file is metAMOS.run
module load metAMOS

initPipeline -q -m file.fastq.12,file2.fastq.12  -d projectDir -i 300:500,1000:2000
runPipeline -k 50 -p 4 -i YES -c phylosift -d projectDir

Then submit, allocating 4 cpus due to the inclusion of the -p 4 option:

slurm --cpus-per-task=4 metAMOS.run