MetAMOS
#
Find similar titles
- (rev. 7)
- Hyungyong Kim
Structured data
- About
- Sequence assembly
- Metagenomics
- Code Repository
- https://github.com/marbl/metAMOS
- Programming Language
- Python
- URL
- http://metamos.readthedocs.org/en/v1.5rc3/index.html
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.
Table of Contents
Installation #
$ wget https://github.com/marbl/metAMOS/archive/v1.5rc3.zip
$ unzip v1.5rc3.zip
$ cd v1.5rc3
$ virtualenv venv
$ source venv/bin/activate
$ python INSTALL.py 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 (Code 0) #
Suggested Pages #
- 0.025 MEGAN
- 0.025 December 1
- 0.025 Frontiers in Genetics
- 0.025
- 0.025 De novo assembly
- 0.025 Frontiers in Plant Science
- 0.025 pandas
- 0.025 January 18
- 0.025 Pfam
- 0.025 De novo transcriptome assembly
- More suggestions...