metaphlan
Link to section 'Introduction' of 'metaphlan' Introduction
MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from 17,000 reference genomes ( 13,500 bacterial and archaeal, 3,500 viral, and 110 eukaryotic), allowing:
- up to 25,000 reads-per-second (on one CPU) analysis speed (orders of magnitude faster compared to existing methods);
- unambiguous taxonomic assignments as the MetaPhlAn markers are clade-specific;
- accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction of reads);
- species-level resolution for bacteria, archaea, eukaryotes and viruses;
- extensive validation of the profiling accuracy on several synthetic datasets and on thousands of real metagenomes.
For more information, please check its user guide at: https://huttenhower.sph.harvard.edu/metaphlan/
Link to section 'Versions' of 'metaphlan' Versions
- 3.0.14
- 3.0.9
- 4.0.2
Commands
metaphlan
Link to section 'Database' of 'metaphlan' Database
The latest version of database(mpa_v30) has been downloaded and built in /depot/itap/datasets/metaphlan/.
Link to section 'Module' of 'metaphlan' Module
You can load the modules by:
module load biocontainers
module load metaphlan/3.0.14
Link to section 'Example job' of 'metaphlan' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run MetaPhlAn on our cluster:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=MetaPhlAn
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers metaphlan/3.0.14
DATABASE=/depot/itap/datasets/metaphlan/
metaphlan SRR11234553_1.fastq,SRR11234553_2.fastq --input_type fastq --nproc 24 -o profiled_metagenome.txt --bowtie2db $DATABASE --bowtie2out metagenome.bowtie2.bz2