MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic sequencing data.
License
Free to use and open source under MIT License.
Available
- Puhti: 4.0.2, 4.0.3, 4.0.6
Usage
To activate MetaPhlAn Puhti, run command:
module load metaphlan
You can check vasic usage with command;
metaphlan --help
MetaPhlAn can automatically retrieve the MetaPhlAn database and create the Bowtie2
indexes it needs on-the-fly when it the command is executed. By default MetaPhlAn
saves these index files to the MetaPhlAn installation directory, but in Puhti,
this is not possible. Because of that, the users should use option --bowtie2db
to define a directory that will be used to store the database and index files.
For example in the case of project_2001234 the user could first create a directory for the databases:
cd /scratch/project_2001234
mkdir metaphlan_databases
Databases can be also be pre-prepared with the --install option:
metaphlan --install --bowtie2db metaphlan_databases
The database is quite big and downloading and building it can take some time.
By default, the latest MetaPhlAn database is downloaded and built. You can download a specific version with the --index parameter.
metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db metaphlan_databases
When running MetaPhlan analyses you must include the --bowtie2db option, and also --index
if using non-default database. If database is not found in the indicated location, it will be automatically generated.
A test input dataset for testing MataPhlAn can be downloaded from the metaphlan github site:
wget https://github.com/biobakery/MetaPhlAn/releases/download/4.0.2/SRS014476-Supragingival_plaque.fasta.gz
In this example the job is executed as an interactive batch job.
sinteractive -m 16G -c 4
module load metaphlan
metaphlan --nproc 4 --bowtie2db metaphlan_databases SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt