MetaPhlAn¶
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.
Profile Format¶
Taxpasta expects a four-column, tab-separated file. This is generated by redirecting the MetaPhlAn3 stdout
. It interprets the columns as:
Column Header | Description |
---|---|
clade_name | |
taxonomy_id | |
relative_abundance | |
additional_species |
Example¶
#mpa_v30_CHOCOPhlAn_201901
#/workspace/nextflow-mentoring/second_pipeline/work/conda/env-e9a987b33d7e880200ff2190a27ad05d/bin/metaphlan ERR525939.trimmed.R1.fastq.gz,ERR525939.trimmed.R2.fastq.gz --bowtie2out metagenome.bowtie2.bz2 --input_type fastq -o ERR525939.taxa.txt
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Bacteria 2 100.0
k__Bacteria|p__Bacteroidetes 2|976 65.30411
k__Bacteria|p__Proteobacteria 2|1224 27.81459
k__Bacteria|p__Firmicutes 2|1239 4.35836
Example¶
# git tag version 3.0.3 | motus version 3.0.3 | map_tax 3.0.3 | gene database: nr3.0.3 | calc_mgc 3.0.3 -y insert.scaled_counts -l 75 | calc_motu 3.0.3 -k mOTU -C no_CAMI -g 3 -c -p | taxonomy: ref_mOTU_3.0.3 meta_mOTU_3.0.3
# call: python /usr/local/bin/../share/motus-3.0.1//motus profile -p -c -f ERX5474932_ERR5766176_1.fastq.gz -r ERX5474932_ERR5766176_2.fastq.gz -db db_mOTU -t 2 -n 2612_pe-ERR5766176-db_mOTU -o 2612_pe-ERR5766176-db_mOTU.out
#consensus_taxonomy NCBI_tax_id 2612_pe-ERR5766176-db_mOTU
Leptospira alexanderi [ref_mOTU_v3_00001] 100053 0
Leptospira weilii [ref_mOTU_v3_00002] 28184 0
Chryseobacterium sp. [ref_mOTU_v3_00004] NA 0