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metAMOS

Description

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.

A typical qsub script would be as follows:

#!/bin/bash
# This file is metAMOS.run
#
#PBS -N metAMOS
#PBS -m be
#PBS -k oe

cd $PBS_O_WORKDIR
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:

qsub -l nodes=1 metAMOS.run

Documentation