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MetaPhlAn2

Description

metaphlan2 website

MetaPhlAn2 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 3,000 reference genomes.

Environment Modules

Run module spider metaphlan2 to find out what environment modules are available for this application.

Environment Variables

  • HPC_METAPHLAN2_DIR - installation directory
  • HPC_METAPHLAN2_BIN - executable directory
  • HPC_METAPHLAN2_DOC - documentation directory
  • HPC_METAPHLAN2_EXE - examples directory

Additional Usage Information

There have been cases where metaphlan tries to download the latest database before running. The latest database mpa_v30_CHOCOPhlAn_201901 is available at $METAPHLAN_BOWTIE2_DB, therefore, to skip the database update step, the following needs to be specified in the script: 

--index mpa_v30_CHOCOPhlAn_201901 --bowtie2db $METAPHLAN_BOWTIE2_DB

Categories

biology, phylogenetics