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. Typemodule 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