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MetaPhlAn: Difference between revisions
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MetaPhlAn is a "computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. | MetaPhlAn is a "computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. | ||
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metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt -nproc $SLURM_CPUS_PER_TASK --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB_DIR --bowtie2out metagenome.bowtie2.bz2 | metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt -nproc $SLURM_CPUS_PER_TASK --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB_DIR --bowtie2out metagenome.bowtie2.bz2 | ||
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