Provided by: metaphlan2_2.7.8-1_all bug

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.