Provided by: metaphlan_4.0.4-1_all 
NAME
metaphlan2 - METAgenomic PHyLogenetic ANalysis for metagenomic taxonomic profiling
SYNOPSIS
metaphlan2
--input_type {fastq,fasta,multifasta,multifastq,bowtie2out,sam} [--mpa_pkl MPA_PKL]
[--bowtie2db METAPHLAN_BOWTIE2_DB] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE]
[--bowtie2out FILE_NAME] [--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len]
[--min_alignment_len] [--ignore_viruses] [--ignore_eukaryotes] [--ignore_bacteria]
[--ignore_archaea] [--stat_q] [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat]
[-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [--clade]
[--min_ab] [-h] [-o output file] [--sample_id_key name] [--sample_id value] [-s
sam_output_file] [--biom biom_output] [--mdelim mdelim] [--nproc N] [-v] [INPUT_FILE]
[OUTPUT_FILE]
DESCRIPTION
MetaPhlAn 2 clade-abundance estimation
The basic usage of MetaPhlAn 2 consists in the identification of the clades (from phyla to
species and strains in particular cases) present in the metagenome obtained from a
microbiome sample and their relative abundance. This correspond to the default analysis
type (--analysis_type rel_ab).
* Profiling a metagenome from raw reads:
metaphlan2 metagenome.fastq --input_type fastq
* You can take advantage of multiple CPUs and save the intermediate BowTie2 output
for re-running
MetaPhlAn extremely quickly:
metaphlan2 metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5
--input_type fastq
* If you already mapped your metagenome against the marker DB (using a previous
MetaPhlAn run), you can obtain the results in few seconds by using the previously
saved --bowtie2out file and specifying the input (--input_type bowtie2out):
metaphlan2 metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out
* You can also provide an externally BowTie2-mapped SAM if you specify this format
with --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the
obtained sam:
bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x
/usr/share/metaphlan2/db_v20/mpa_v20_m200 -U metagenome.fastq metaphlan2
metagenome.sam --input_type sam > profiled_metagenome.txt
* Multiple alternative ways to pass the input are also available:
cat metagenome.fastq | metaphlan2 --input_type fastq
tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2 --input_type fastq
metaphlan2 --input_type fastq < metagenome.fastq
metaphlan2 --input_type fastq <(bzcat metagenome.fastq.bz2)
metaphlan2 --input_type fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz)
* We can also natively handle paired-end metagenomes, and, more generally,
metagenomes stored in multiple files (but you need to specify the --bowtie2out
parameter):
metaphlan2 metagenome_1.fastq,metagenome_2.fastq --bowtie2out
metagenome.bowtie2.bz2 --nproc 5 --input_type fastq
MetaPhlAn 2 strain tracking
MetaPhlAn 2 introduces the capability of charachterizing organisms at the strain level
using non aggregated marker information. Such capability comes with several slightly
different flavours and are a way to perform strain tracking and comparison across multiple
samples. Usually, MetaPhlAn 2 is first ran with the default --analysis_type to profile
the species present in the community, and then a strain-level profiling can be performed
to zoom-in into specific species of interest. This operation can be performed quickly as
it exploits the --bowtie2out intermediate file saved during the execution of the default
analysis type.
* The following command will output the abundance of each marker with a RPK (reads
per kil-base) higher 0.0. (we are assuming that metagenome_outfmt.bz2 has been
generated before as shown above).
metaphlan2 -t marker_ab_table metagenome_outfmt.bz2 --input_type bowtie2out >
marker_abundance_table.txt
The obtained RPK can be optionally normalized by the total number of reads in the
metagenome to guarantee fair comparisons of abundances across samples. The number
of reads in the metagenome needs to be passed with the '--nreads' argument
* The list of markers present in the sample can be obtained with '-t
marker_pres_table'
metaphlan2 -t marker_pres_table metagenome_outfmt.bz2 --input_type bowtie2out >
marker_abundance_table.txt
The --pres_th argument (default 1.0) set the minimum RPK value to consider a marker
present
* The list '-t clade_profiles' analysis type reports the same information of '-t
marker_ab_table' but the markers are reported on a clade-by-clade basis.
metaphlan2 -t clade_profiles metagenome_outfmt.bz2 --input_type bowtie2out >
marker_abundance_table.txt
* Finally, to obtain all markers present for a specific clade and all its subclades,
the '-t clade_specific_strain_tracker' should be used. For example, the following
command is reporting the presence/absence of the markers for the B. fragulis
species and its strains the optional argument --min_ab specifies the minimum clade
abundance for reporting the markers
$ metaphlan2 -t clade_specific_strain_tracker --clade s__Bacteroides_fragilis
metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
OPTIONS
positional arguments
INPUT_FILE
the input file can be:
* a fastq file containing metagenomic reads
OR
* a BowTie2 produced SAM file.
OR
* an intermediary mapping file of the metagenome generated by a previous MetaPhlAn
run
If the input file is missing, the script assumes that the input is provided using
the standard input, or named pipes. IMPORTANT: the type of input needs to be
specified with --input_type
OUTPUT_FILE
the tab-separated output file of the predicted taxon relative abundances [stdout if
not present]
Required arguments
--input_type {fastq,fasta,multifasta,multifastq,bowtie2out,sam}
set whether the input is the multifasta file of metagenomic reads or the SAM file
of the mapping of the reads against the MetaPhlAn db. [default 'automatic', i.e.
the script will try to guess the input format]
Mapping arguments:
--mpa_pkl MPA_PKL
the metadata pickled MetaPhlAn file
--bowtie2db METAPHLAN_BOWTIE2_DB
The BowTie2 database file of the MetaPhlAn database. Used if --input_type is
fastq, fasta, multifasta, or multifastq
--bt2_ps BowTie2 presets
presets options for BowTie2 (applied only when a multifasta file is provided) The
choices enabled in MetaPhlAn are:
* sensitive
* very-sensitive
* sensitive-local
* very-sensitive-local
[default very-sensitive]
--bowtie2_exe BOWTIE2_EXE
Full path and name of the BowTie2 executable. This option allows MetaPhlAn to reach
the executable even when it is not in the system PATH or the system PATH is
unreachable
--bowtie2out FILE_NAME
The file for saving the output of BowTie2
--no_map
Avoid storing the --bowtie2out map file
--tmp_dir
the folder used to store temporary files [default is the OS dependent tmp dir]
Post-mapping arguments
--tax_lev TAXONOMIC_LEVEL
The taxonomic level for the relative abundance output:
'a' : all taxonomic levels
'k' : kingdoms
'p' : phyla only
'c' : classes only
'o' : orders only
'f' : families only
'g' : genera only
's' : species only
[default 'a']
--min_cu_len
minimum total nucleotide length for the markers in a clade for estimating the
abundance without considering sub-clade abundances [default 2000]
--min_alignment_len
The sam records for aligned reads with the longest subalignment length smaller than
this threshold will be discarded. [default None]
--ignore_viruses
Do not profile viral organisms
--ignore_eukaryotes
Do not profile eukaryotic organisms
--ignore_bacteria
Do not profile bacterial organisms
--ignore_archaea
Do not profile archeal organisms
--stat_q
Quantile value for the robust average [default 0.1]
--ignore_markers IGNORE_MARKERS
File containing a list of markers to ignore.
--avoid_disqm
Deactivate the procedure of disambiguating the quasi-markers based on the marker
abundance pattern found in the sample. It is generally recommended too keep the
disambiguation procedure in order to minimize false positives
--stat EXPERIMENTAL! Statistical approach for converting marker abundances into clade
abundances
'avg_g' : clade global (i.e. normalizing all markers together) average
'avg_l' : average of length-normalized marker counts
'tavg_g' : truncated clade global average at --stat_q quantile
'tavg_l' : trunated average of length-normalized marker counts (at --stat_q)
'wavg_g' : winsorized clade global average (at --stat_q)
'wavg_l' : winsorized average of length-normalized marker counts (at --stat_q)
'med' : median of length-normalized marker counts
[default tavg_g]
Additional analysis types and arguments
-t ANALYSIS TYPE
Type of analysis to perform:
* rel_ab: profiling a metagenomes in terms of relative abundances
* rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and
estimate the number of reads coming from each clade.
* reads_map: mapping from reads to clades (only reads hitting a marker)
* clade_profiles: normalized marker counts for clades with at least a non-null marker
* marker_ab_table: normalized marker counts (only when > 0.0 and normalized by
metagenome size if --nreads is specified)
* marker_counts: non-normalized marker counts [use with extreme caution]
* marker_pres_table: list of markers present in the sample (threshold at 1.0 if not
differently specified with --pres_th
[default 'rel_ab']
--nreads NUMBER_OF_READS
The total number of reads in the original metagenome. It is used only when -t
marker_table is specified for normalizing the length-normalized counts with the
metagenome size as well. No normalization applied if --nreads is not specified
--pres_th PRESENCE_THRESHOLD
Threshold for calling a marker present by the -t marker_pres_table option
--clade
The clade for clade_specific_strain_tracker analysis
--min_ab
The minimum percentage abundace for the clade in the clade_specific_strain_tracker
analysis
-h, --help
show this help message and exit
Output arguments
-o output file, --output_file output file
The output file (if not specified as positional argument)
--sample_id_key name
Specify the sample ID key for this analysis. Defaults to '#SampleID'.
--sample_id value
Specify the sample ID for this analysis. Defaults to 'Metaphlan2_Analysis'.
-s sam_output_file, --samout sam_output_file
The sam output file
--biom biom_output, --biom_output_file biom_output
If requesting biom file output: The name of the output file in biom format
--mdelim mdelim, --metadata_delimiter_char mdelim
Delimiter for bug metadata: - defaults to pipe. e.g. the pipe in
k__Bacteria|p__Proteobacteria
Other arguments
--nproc N
The number of CPUs to use for parallelizing the mapping [default 1, i.e. no
parallelism]
-v, --version
Prints the current MetaPhlAn version and exit
AUTHOR
The code of MetaPhlAn was rwitten by Nicola Segata (nicola.segata@unitn.it), Duy Tin
Truong (duytin.truong@unitn.it).
This manpage was written by Andreas Tille for the Debian distribution and can be used for
any other usage of the program.