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AMOS for Metagenomics. It replace Bambus2.

MetAMOS represents a focused effort to create automated, reproducible, traceable assembly & analysis infused with current best practices and state-of-the-art methods.

MetAMOS for input can start with next-generation sequencing reads or assemblies, and as output, produces: assembly reports, genomic scaffolds, open-reading frames, variant motifs, taxonomic or functional annotations, Krona charts and HTML report.

Installation #

$ wget
$ unzip
$ cd v1.5rc3
$ virtualenv venv
$ source venv/bin/activate
$ python core

Usage #

$ initPipeline -f/-q -1 file.fastq.1 -2 file.fastq.2 -d projectDir -i 300:500
$ runPipeline -d projectDir

Example #

Get data using SRA Tools (split paired files)

$ fastq-dump SRR041654 --split-files 
$ fastq-dump SRR041655 --split-files
$ fastq-dump SRR041656 --split-files
$ fastq-dump SRR041657 --split-files

Execute MetAMOS

$ time initPipeline -q -1 SRR041654_1.fastq,SRR041655_1.fastq,SRR041656_1.fastq,SRR041657_1.fastq -2 SRR041654_2.fastq,SRR041655_2.fastq,SRR041656_2.fastq,SRR041657_2.fastq -d metamos_out -i 0:10,0:10,0:10,0:10
real    8m2.105s
user    0m3.610s
sys     0m42.692s
$ time runPipeline -d metamos_out2 -p 20

Important options #

Assembly statistics #

Reference #

Incoming Links #

Related Codes #

Suggested Pages #