What is iMetAMOS¶
iMetAMOS is an extension of metAMOS to isolate genome assembly. It is a workflow which, by default, uses multiple assemblers and validation tools to select the best assembly for a given sample. Effectively, this is equivalent to GAGE-in-a-box or ensemble assembly. iMetAMOS is included in the frozen binary.
If you have used iMetAMOS for analyzing your, please cite (in addition to the individual software component citations listed in main output):
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 15:126, 2014.
Please also consider citing the original metAMOS publication:
Treangen TJ\*, Koren S\*, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013 Jan 15;14(1):R2. PMID: 23320958.
*Indicates both authors contributed equally to this work
To install iMetAMOS without using a frozen binary, run:
$ curl -L https://github.com/marbl/metAMOS/archive/v1.5rc3 > v1.5rc3.zip $ unzip v1.5rc3.zip $ cd metAMOS-v1.5rc3 $ python INSTALL.py iMetAMOS
To enable iMetAMOS, specify it as an option to initPipeline using the -W flag. Below is a simple example of running of iMetAMOS to assemble an SRA dataset:
initPipeline -q -1 SRR987657 -d projectDir -W iMetAMOS runPipeline -d projectDir -p 16