modules/metaphlan_metaphlan
MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
Description
MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
Input
Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.
Note that you will also need to specify --index and the database version name (e.g. ‘mpa_vJan21_TOY_CHOCOPhlAnSGB_202103’) in your module.conf ext.args for METAPHLAN_METAPHLAN!
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