metaphlanblastMetagenomic Phylogenetic Analysis
metaphlan.py
#if str($source.type) == "fasta":
${source.fasta_input}
#else:
${source.blast_input}
#end if
${metaphlan_out}
--nproc 4
#if str($source.type) == "fasta":
--blastout metagenome.outfmt6.txt
--evalue ${source.evalue}
#end if
--lib_dir ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan
--min_cu_len ${min_cu_len}
--min_nreads ${min_nreads}
source['type'] == "fasta"
**What it does**
MetaPhlAn 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 reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.
MetaPhlAn main features are:
More than 100x computational speedup compared to Blast-based approaches or other available methods with species level resolution
Higher accuracy in estimating the true composition of microbial communities in terms of organismal relative abundance
Unambiguous read-to-taxa assignments as conserved inter-clade sequences are removed from the reference sequence data
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**Inputs**
The input file can be a multi-fasta file containing metagenomic reads OR a NCBI BLAST output file (-outfmt 6 format) of the metagenomic read fasta file against the metaflan database.
**outputs**
The output is a tab-separated output file of the predicted taxon relative abundances.
If the input is a multi-fasta file then the output from the BLAST operation is also provided as an additional output.
---------
**Settings**::
--tax_lev TAXONOMIC_LEVEL
The taxonomic level for the relative abundance
output:
'a' : all taxonomic levels
'k' : kingdoms (Bacteria and Archaea) only
'p' : phyla only
'c' : classes only
'o' : orders only
'f' : families only
'g' : genera only
's' : species only
[default 'a']
--evalue evalue threshold for the blasting
[default 1e-6]
--min_cu_len minimum total nucleotide lenght for the unique
markers for estimating the abundance without
considering children clade abundances
[default 10000]
--min_nreads minimum total reads assigned to a clade for
estimating the abundance without considering
children clade abundances
[default 5]
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**Citation**
If you find MetaPhlAn useful in your research, please cite our paper:
Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower.
"Fast and accurate metagenomic profiling of microbial community composition using unique clade-specific marker genes"
***in review***