ganon 
:)
Code: GitHub repository
ganon is designed to index large sets of genomic reference sequences and to classify reads against them efficiently. The tool uses Hierarchical Interleaved Bloom Filters as indices based on k-mers with optional minimizers. It was mainly developed, but not limited, to the metagenomics classification problem: quickly assign sequence fragments to their closest reference among thousands of references. After classification, taxonomic or sequence abundances are estimated and reported.
Features:)
- integrated download and build of any subset from RefSeq/Genbank/GTDB with incremental updates
- NCBI and GTDB native support for taxonomic classification, custom taxonomy or no taxonomy at all
- customizable database build for local or non-standard sequence files
- optimized taxonomic binning and profiling configurations
- build and classify at various taxonomic levels, strain, assembly, file, sequence or custom specialization
- hierarchical classification using several databases in one or more levels in just one run
- EM and/or LCA algorithms to solve multiple-matching reads
- reporting of multiple and unique matches for every read
- reporting of sequence, taxonomic or multi-match abundances with optional genome size correction
- advanced tree-like reports with several filter options
- generation of contingency tables with several filters for multi-sample studies
ganon achieved very good results in our own evaluations but also in independent evaluations: LEMMI, LEMMI v2 and CAMI2
Installation with conda:)
The easiest way to install ganon is via conda, using the bioconda and conda-forge channels:
conda install -c bioconda -c conda-forge ganon
However, there are possible performance benefits compiling ganon from source in the target machine rather than using the conda version. To do so, please follow the instructions below:
Installation from source:)
Python dependencies:)
- python >=3.6
- pandas >=1.2.0
- multitax >=1.3.1
- genome_updater >=0.6.3
# Python version should be >=3.6
python3 -V
# Install packages via pip or conda:
# PIP
python3 -m pip install "pandas>=1.2.0" "multitax>=1.3.1"
wget --quiet --show-progress https://raw.githubusercontent.com/pirovc/genome_updater/master/genome_updater.sh && chmod +x genome_updater.sh
# Conda/Mamba (alternative)
conda install -c bioconda -c conda-forge "pandas>=1.2.0" "multitax>=1.3.1" "genome_updater>=0.6.3"
C++ dependencies:)
- GCC >=11
- CMake >=3.4
- zlib
- bzip2
- raptor ==3.0.1
Tip
If your system has GCC version 10 or below, you can create an environment with the latest conda-forge GCC version and dependencies: conda create -c conda-forge -n gcc-conda gcc gxx zlib bzip2 cmake and activate the environment with: source activate gcc-conda.
In CMake, you may have set the environment include directory with the following parameter: -DSEQAN3_CXX_FLAGS="-I/path/to/miniconda3/envs/gcc-conda/include/" changing /path/to/miniconda3 with your local path to the conda installation.
Downloading and building ganon + submodules:)
git clone --recurse-submodules https://github.com/pirovc/ganon.git
# Install Python side
cd ganon
python3 setup.py install --record files.txt # optional
# Compile and install C++ side
mkdir -p build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DVERBOSE_CONFIG=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCONDA=OFF -DLONGREADS=OFF ..
make -j 4
sudo make install # optional
- to change install location (e.g.
/myprefix/bin/), set the installation prefix in the cmake command with-DCMAKE_INSTALL_PREFIX=/myprefix/ - use
-DINCLUDE_DIRSto set alternative paths to cxxopts and Catch2 libs. - to classify extremely large reads or contigs that would need more than 65000 k-mers, use
-DLONGREADS=ON
Installing raptor:)
The easiest way to install raptor is via conda with conda install -c bioconda -c conda-forge "raptor=3.0.1" (already included in ganon install via conda).
Note
raptor is required to build databases with the Hierarchical Interleaved Bloom Filter (ganon build --filter-type hibf)
To build old style ganon indices ganon build --filter-type ibf, raptor is not required
To install raptor from source, follow the instructions below:
Dependencies:)
- CMake >= 3.18
- GCC 11, 12 or 13 (most recent minor version)
Downloading and building raptor + submodules:)
git clone --branch raptor-v3.0.1 --recurse-submodules https://github.com/seqan/raptor
cd raptor
mkdir -p build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-std=c++23 -Wno-interference-size" ..
make -j 4
- binaries will be located in the
bindirectory - you may have to inform
ganon buildthe path to the binaries with--raptor-path raptor/build/bin
Testing:)
If everything was properly installed, the following command should show the help pages without errors:
ganon -h
Running tests:)
python3 -m pip install "parameterized>=0.9.0" # Alternative: conda install -c conda-forge "parameterized>=0.9.0"
python3 -m unittest discover -s tests/ganon/integration/
python3 -m unittest discover -s tests/ganon/integration_online/ # optional - downloads large files
cd build/
ctest -VV .
Parameters:)
usage: ganon [-h] [-v]
{build,build-custom,update,classify,reassign,report,table} ...
- - - - - - - - - -
_ _ _ _ _
(_|(_|| |(_)| |
_| v. 2.1.0
- - - - - - - - - -
positional arguments:
{build,build-custom,update,classify,reassign,report,table}
build Download and build ganon default databases
(refseq/genbank)
build-custom Build custom ganon databases
update Update ganon default databases
classify Classify reads against built databases
reassign Reassign reads with multiple matches with an EM
algorithm
report Generate reports from classification results
table Generate table from reports
options:
-h, --help show this help message and exit
-v, --version Show program's version number and exit.
ganon build
usage: ganon build [-h] [-g [...]] [-a [...]] [-l] [-b [...]] [-o] [-c] [-r] [-u] [-m [...]] [-z [...]]
[--skip-genome-size] -d DB_PREFIX [-x] [-t] [-p] [-k] [-w] [-s] [-f] [-j] [-y] [-v] [--restart]
[--verbose] [--quiet] [--write-info-file]
options:
-h, --help show this help message and exit
required arguments:
-g [ ...], --organism-group [ ...]
One or more organism groups to download [archaea, bacteria, fungi, human, invertebrate,
metagenomes, other, plant, protozoa, vertebrate_mammalian, vertebrate_other, viral]. Mutually
exclusive --taxid (default: None)
-a [ ...], --taxid [ ...]
One or more taxonomic identifiers to download. e.g. 562 (-x ncbi) or 's__Escherichia coli' (-x
gtdb). Mutually exclusive --organism-group (default: None)
-d DB_PREFIX, --db-prefix DB_PREFIX
Database output prefix (default: None)
database arguments:
-l , --level Highest level to build the database. Options: any available taxonomic rank [species, genus,
...], 'leaves' for taxonomic leaves or 'assembly' for a assembly/strain based analysis (default:
species)
download arguments:
-b [ ...], --source [ ...]
Source to download [refseq, genbank] (default: ['refseq'])
-o , --top Download limited assemblies for each taxa. 0 for all. (default: 0)
-c, --complete-genomes
Download only sub-set of complete genomes (default: False)
-r, --representative-genomes
Download only sub-set of representative genomes (default: False)
-u , --genome-updater
Additional genome_updater parameters (https://github.com/pirovc/genome_updater) (default: None)
-m [ ...], --taxonomy-files [ ...]
Specific files for taxonomy - otherwise files will be downloaded (default: None)
-z [ ...], --genome-size-files [ ...]
Specific files for genome size estimation - otherwise files will be downloaded (default: None)
--skip-genome-size Do not attempt to get genome sizes. Activate this option when using sequences not representing
full genomes. (default: False)
important arguments:
-x , --taxonomy Set taxonomy to enable taxonomic classification, lca and reports [ncbi, gtdb, skip] (default:
ncbi)
-t , --threads
advanced arguments:
-p , --max-fp Max. false positive for bloom filters. Mutually exclusive --filter-size. Defaults to 0.001 with
--filter-type hibf or 0.05 with --filter-type ibf. (default: None)
-k , --kmer-size The k-mer size to split sequences. (default: 19)
-w , --window-size The window-size to build filter with minimizers. (default: 31)
-s , --hash-functions
The number of hash functions for the interleaved bloom filter [1-5]. With --filter-type ibf, 0
will try to set optimal value. (default: 4)
-f , --filter-size Fixed size for filter in Megabytes (MB). Mutually exclusive --max-fp. Only valid for --filter-
type ibf. (default: 0)
-j , --mode Create smaller or faster filters at the cost of classification speed or database size,
respectively [avg, smaller, smallest, faster, fastest]. If --filter-size is used,
smaller/smallest refers to the false positive rate. By default, an average value is calculated
to balance classification speed and database size. Only valid for --filter-type ibf. (default:
avg)
-y , --min-length Skip sequences smaller then value defined. 0 to not skip any sequence. Only valid for --filter-
type ibf. (default: 0)
-v , --filter-type Variant of bloom filter to use [hibf, ibf]. hibf requires raptor >= v3.0.1 installed or binary
path set with --raptor-path. --mode, --filter-size and --min-length will be ignored with hibf.
hibf will set --max-fp 0.001 as default. (default: hibf)
optional arguments:
--restart Restart build/update from scratch, do not try to resume from the latest possible step.
{db_prefix}_files/ will be deleted if present. (default: False)
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
--write-info-file Save copy of target info generated to {db_prefix}.info.tsv. Can be re-used as --input-file for
further attempts. (default: False)
ganon build-custom
usage: ganon build-custom [-h] [-i [...]] [-e] [-c] [-n] [-a] [-l] [-m [...]] [-z [...]] [--skip-genome-size] [-r [...]]
[-q [...]] -d DB_PREFIX [-x] [-t] [-p] [-k] [-w] [-s] [-f] [-j] [-y] [-v] [--restart]
[--verbose] [--quiet] [--write-info-file]
options:
-h, --help show this help message and exit
required arguments:
-i [ ...], --input [ ...]
Input file(s) and/or folder(s). Mutually exclusive --input-file. (default: None)
-e , --input-extension
Required if --input contains folder(s). Wildcards/Shell Expansions not supported (e.g. *).
(default: fna.gz)
-c, --input-recursive
Look for files recursively in folder(s) provided with --input (default: False)
-d DB_PREFIX, --db-prefix DB_PREFIX
Database output prefix (default: None)
custom arguments:
-n , --input-file Tab-separated file with all necessary file/sequence information. Fields: file [<tab> target
<tab> node <tab> specialization <tab> specialization name]. For details:
https://pirovc.github.io/ganon/custom_databases/. Mutually exclusive --input (default: None)
-a , --input-target Target to use [file, sequence]. Parse input by file or by sequence. Using 'file' is recommended
and will speed-up the building process (default: file)
-l , --level Max. level to build the database. By default, --level is the --input-target. Options: any
available taxonomic rank [species, genus, ...] or 'leaves' (requires --taxonomy). Further
specialization options [assembly, custom]. assembly will retrieve and use the assembly accession
and name. custom requires and uses the specialization field in the --input-file. (default: None)
-m [ ...], --taxonomy-files [ ...]
Specific files for taxonomy - otherwise files will be downloaded (default: None)
-z [ ...], --genome-size-files [ ...]
Specific files for genome size estimation - otherwise files will be downloaded (default: None)
--skip-genome-size Do not attempt to get genome sizes. Activate this option when using sequences not representing
full genomes. (default: False)
ncbi arguments:
-r [ ...], --ncbi-sequence-info [ ...]
Uses NCBI e-utils webservices or downloads accession2taxid files to extract target information.
[eutils, nucl_gb, nucl_wgs, nucl_est, nucl_gss, pdb, prot, dead_nucl, dead_wgs, dead_prot or one
or more accession2taxid files from https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/].
By default uses e-utils up-to 50000 sequences or downloads nucl_gb nucl_wgs otherwise. (default:
[])
-q [ ...], --ncbi-file-info [ ...]
Downloads assembly_summary files to extract target information. [refseq, genbank,
refseq_historical, genbank_historical or one or more assembly_summary files from
https://ftp.ncbi.nlm.nih.gov/genomes/] (default: ['refseq', 'genbank'])
important arguments:
-x , --taxonomy Set taxonomy to enable taxonomic classification, lca and reports [ncbi, gtdb, skip] (default:
ncbi)
-t , --threads
advanced arguments:
-p , --max-fp Max. false positive for bloom filters. Mutually exclusive --filter-size. Defaults to 0.001 with
--filter-type hibf or 0.05 with --filter-type ibf. (default: None)
-k , --kmer-size The k-mer size to split sequences. (default: 19)
-w , --window-size The window-size to build filter with minimizers. (default: 31)
-s , --hash-functions
The number of hash functions for the interleaved bloom filter [1-5]. With --filter-type ibf, 0
will try to set optimal value. (default: 4)
-f , --filter-size Fixed size for filter in Megabytes (MB). Mutually exclusive --max-fp. Only valid for --filter-
type ibf. (default: 0)
-j , --mode Create smaller or faster filters at the cost of classification speed or database size,
respectively [avg, smaller, smallest, faster, fastest]. If --filter-size is used,
smaller/smallest refers to the false positive rate. By default, an average value is calculated
to balance classification speed and database size. Only valid for --filter-type ibf. (default:
avg)
-y , --min-length Skip sequences smaller then value defined. 0 to not skip any sequence. Only valid for --filter-
type ibf. (default: 0)
-v , --filter-type Variant of bloom filter to use [hibf, ibf]. hibf requires raptor >= v3.0.1 installed or binary
path set with --raptor-path. --mode, --filter-size and --min-length will be ignored with hibf.
hibf will set --max-fp 0.001 as default. (default: hibf)
optional arguments:
--restart Restart build/update from scratch, do not try to resume from the latest possible step.
{db_prefix}_files/ will be deleted if present. (default: False)
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
--write-info-file Save copy of target info generated to {db_prefix}.info.tsv. Can be re-used as --input-file for
further attempts. (default: False)
ganon update
usage: ganon update [-h] -d DB_PREFIX [-o] [-t] [--restart] [--verbose] [--quiet] [--write-info-file]
options:
-h, --help show this help message and exit
required arguments:
-d DB_PREFIX, --db-prefix DB_PREFIX
Existing database input prefix (default: None)
important arguments:
-o , --output-db-prefix
Output database prefix. By default will be the same as --db-prefix and overwrite files (default:
None)
-t , --threads
optional arguments:
--restart Restart build/update from scratch, do not try to resume from the latest possible step.
{db_prefix}_files/ will be deleted if present. (default: False)
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
--write-info-file Save copy of target info generated to {db_prefix}.info.tsv. Can be re-used as --input-file for
further attempts. (default: False)
ganon classify
usage: ganon classify [-h] -d [DB_PREFIX ...] [-s [reads.fq[.gz] ...]] [-p [reads.1.fq[.gz] reads.2.fq[.gz] ...]]
[-c [...]] [-e [...]] [-m] [--ranks [...]] [--min-count] [--report-type] [--skip-report] [-o]
[--output-one] [--output-all] [--output-unclassified] [--output-single] [-t] [-b] [-f [...]]
[-l [...]] [--verbose] [--quiet]
options:
-h, --help show this help message and exit
required arguments:
-d [DB_PREFIX ...], --db-prefix [DB_PREFIX ...]
Database input prefix[es] (default: None)
-s [reads.fq[.gz] ...], --single-reads [reads.fq[.gz] ...]
Multi-fastq[.gz] file[s] to classify (default: None)
-p [reads.1.fq[.gz] reads.2.fq[.gz] ...], --paired-reads [reads.1.fq[.gz] reads.2.fq[.gz] ...]
Multi-fastq[.gz] pairs of file[s] to classify (default: None)
cutoff/filter arguments:
-c [ ...], --rel-cutoff [ ...]
Min. percentage of a read (set of k-mers) shared with a reference necessary to consider a match.
Generally used to remove low similarity matches. Single value or one per database (e.g. 0.7 1
0.25). 0 for no cutoff (default: [0.75])
-e [ ...], --rel-filter [ ...]
Additional relative percentage of matches (relative to the best match) to keep. Generally used
to keep top matches above cutoff. Single value or one per hierarchy (e.g. 0.1 0). 1 for no
filter (default: [0.1])
post-processing/report arguments:
-m , --multiple-matches
Method to solve reads with multiple matches [em, lca, skip]. em -> expectation maximization
algorithm based on unique matches. lca -> lowest common ancestor based on taxonomy. The EM
algorithm can be executed later with 'ganon reassign' using the .all file (--output-all).
(default: em)
--ranks [ ...] Ranks to report taxonomic abundances (.tre). empty will report default ranks [superkingdom,
phylum, class, order, family, genus, species, assembly]. (default: [])
--min-count Minimum percentage/counts to report an taxa (.tre) [use values between 0-1 for percentage, >1
for counts] (default: 5e-05)
--report-type Type of report (.tre) [abundance, reads, matches, dist, corr]. More info in 'ganon report'.
(default: abundance)
--skip-report Disable tree-like report (.tre) at the end of classification. Can be done later with 'ganon
report'. (default: False)
output arguments:
-o , --output-prefix
Output prefix for output (.rep) and tree-like report (.tre). Empty to output to STDOUT (only
.rep) (default: None)
--output-one Output a file with one match for each read (.one) either an unique match or a result from the EM
or a LCA algorithm (--multiple-matches) (default: False)
--output-all Output a file with all unique and multiple matches (.all) (default: False)
--output-unclassified
Output a file with unclassified read headers (.unc) (default: False)
--output-single When using multiple hierarchical levels, output everything in one file instead of one per
hierarchy (default: False)
other arguments:
-t , --threads Number of sub-processes/threads to use (default: 1)
-b, --binning Optimized parameters for binning (--rel-cutoff 0.25 --rel-filter 0 --min-count 0 --report-type
reads). Will report sequence abundances (.tre) instead of tax. abundance. (default: False)
-f [ ...], --fpr-query [ ...]
Max. false positive of a query to accept a match. Applied after --rel-cutoff and --rel-filter.
Generally used to remove false positives matches querying a database build with large --max-fp.
Single value or one per hierarchy (e.g. 0.1 0). 1 for no filter (default: [1e-05])
-l [ ...], --hierarchy-labels [ ...]
Hierarchy definition of --db-prefix files to be classified. Can also be a string, but input will
be sorted to define order (e.g. 1 1 2 3). The default value reported without hierarchy is 'H1'
(default: None)
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
ganon reassign
usage: ganon reassign [-h] -i -o OUTPUT_PREFIX [-e] [-s] [--remove-all] [--skip-one] [--verbose] [--quiet]
options:
-h, --help show this help message and exit
required arguments:
-i , --input-prefix Input prefix to find files from ganon classify (.all and optionally .rep) (default: None)
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Output prefix for reassigned file (.one and optionally .rep). In case of multiple files, the
base input filename will be appended at the end of the output file 'output_prefix +
FILENAME.out' (default: None)
EM arguments:
-e , --max-iter Max. number of iterations for the EM algorithm. If 0, will run until convergence (check
--threshold) (default: 10)
-s , --threshold Convergence threshold limit to stop the EM algorithm. (default: 0)
other arguments:
--remove-all Remove input file (.all) after processing. (default: False)
--skip-one Do not write output file (.one) after processing. (default: False)
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
ganon report
usage: ganon report [-h] -i [...] [-e INPUT_EXTENSION] -o OUTPUT_PREFIX [-d [...]] [-x] [-m [...]] [-z [...]]
[--skip-genome-size] [-f] [-t] [-r [...]] [-s] [-a] [-y] [-p [...]] [-k [...]] [-c] [--verbose]
[--quiet] [--min-count] [--max-count] [--names [...]] [--names-with [...]] [--taxids [...]]
options:
-h, --help show this help message and exit
required arguments:
-i [ ...], --input [ ...]
Input file(s) and/or folder(s). '.rep' file(s) from ganon classify. (default: None)
-e INPUT_EXTENSION, --input-extension INPUT_EXTENSION
Required if --input contains folder(s). Wildcards/Shell Expansions not supported (e.g. *).
(default: rep)
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Output prefix for report file 'output_prefix.tre'. In case of multiple files, the base input
filename will be appended at the end of the output file 'output_prefix + FILENAME.tre' (default:
None)
db/tax arguments:
-d [ ...], --db-prefix [ ...]
Database prefix(es) used for classification. Only '.tax' file(s) are required. If not provided,
new taxonomy will be downloaded. Mutually exclusive with --taxonomy. (default: [])
-x , --taxonomy Taxonomy database to use [ncbi, gtdb, skip]. Mutually exclusive with --db-prefix. (default:
ncbi)
-m [ ...], --taxonomy-files [ ...]
Specific files for taxonomy - otherwise files will be downloaded (default: None)
-z [ ...], --genome-size-files [ ...]
Specific files for genome size estimation - otherwise files will be downloaded (default: None)
--skip-genome-size Do not attempt to get genome sizes. Valid only without --db-prefix. Activate this option when
using sequences not representing full genomes. (default: False)
output arguments:
-f , --output-format
Output format [text, tsv, csv, bioboxes]. text outputs a tabulated formatted text file for
better visualization. bioboxes is the the CAMI challenge profiling format (only
percentage/abundances are reported). (default: tsv)
-t , --report-type Type of report [abundance, reads, matches, dist, corr]. 'abundance' -> tax. abundance (re-
distribute read counts and correct by genome size), 'reads' -> sequence abundance, 'matches' ->
report all unique and shared matches, 'dist' -> like reads with re-distribution of shared read
counts only, 'corr' -> like abundance without re-distribution of shared read counts (default:
abundance)
-r [ ...], --ranks [ ...]
Ranks to report ['', 'all', custom list]. 'all' for all possible ranks. empty for default ranks
[superkingdom, phylum, class, order, family, genus, species, assembly]. (default: [])
-s , --sort Sort report by [rank, lineage, count, unique]. Default: rank (with custom --ranks) or lineage
(with --ranks all) (default: )
-a, --no-orphan Omit orphan nodes from the final report. Otherwise, orphan nodes (= nodes not found in the
db/tax) are reported as 'na' with root as direct parent. (default: False)
-y, --split-hierarchy
Split output reports by hierarchy (from ganon classify --hierarchy-labels). If activated, the
output files will be named as '{output_prefix}.{hierarchy}.tre' (default: False)
-p [ ...], --skip-hierarchy [ ...]
One or more hierarchies to skip in the report (from ganon classify --hierarchy-labels) (default:
[])
-k [ ...], --keep-hierarchy [ ...]
One or more hierarchies to keep in the report (from ganon classify --hierarchy-labels) (default:
[])
-c , --top-percentile
Top percentile filter, based on percentage/relative abundance. Applied only at default ranks
[superkingdom, phylum, class, order, family, genus, species, assembly] (default: 0)
optional arguments:
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
filter arguments:
--min-count Minimum number/percentage of counts to keep an taxa [values between 0-1 for percentage, >1
specific number] (default: 0)
--max-count Maximum number/percentage of counts to keep an taxa [values between 0-1 for percentage, >1
specific number] (default: 0)
--names [ ...] Show only entries matching exact names of the provided list (default: [])
--names-with [ ...] Show entries containing full or partial names of the provided list (default: [])
--taxids [ ...] One or more taxids to report (including children taxa) (default: [])
ganon table
usage: ganon table [-h] -i [...] [-e] -o OUTPUT_FILE [-l] [-f] [-t] [-a] [-m] [-r] [-n] [--header]
[--unclassified-label] [--filtered-label] [--skip-zeros] [--transpose] [--verbose] [--quiet]
[--min-count] [--max-count] [--names [...]] [--names-with [...]] [--taxids [...]]
options:
-h, --help show this help message and exit
required arguments:
-i [ ...], --input [ ...]
Input file(s) and/or folder(s). '.tre' file(s) from ganon report. (default: None)
-e , --input-extension
Required if --input contains folder(s). Wildcards/Shell Expansions not supported (e.g. *).
(default: tre)
-o OUTPUT_FILE, --output-file OUTPUT_FILE
Output filename for the table (default: None)
output arguments:
-l , --output-value Output value on the table [percentage, counts]. percentage values are reported between [0-1]
(default: counts)
-f , --output-format
Output format [tsv, csv] (default: tsv)
-t , --top-sample Top hits of each sample individually (default: 0)
-a , --top-all Top hits of all samples (ranked by percentage) (default: 0)
-m , --min-frequency
Minimum number/percentage of files containing an taxa to keep the taxa [values between 0-1 for
percentage, >1 specific number] (default: 0)
-r , --rank Define specific rank to report. Empty will report all ranks. (default: None)
-n, --no-root Do not report root node entry and lineage. Direct and shared matches to root will be accounted
as unclassified (default: False)
--header Header information [name, taxid, lineage] (default: name)
--unclassified-label
Add column with unclassified count/percentage with the chosen label. May be the same as
--filtered-label (e.g. unassigned) (default: None)
--filtered-label Add column with filtered count/percentage with the chosen label. May be the same as
--unclassified-label (e.g. unassigned) (default: None)
--skip-zeros Do not print lines with only zero count/percentage (default: False)
--transpose Transpose output table (taxa as cols and files as rows) (default: False)
optional arguments:
--verbose Verbose output mode (default: False)
--quiet Quiet output mode (default: False)
filter arguments:
--min-count Minimum number/percentage of counts to keep an taxa [values between 0-1 for percentage, >1
specific number] (default: 0)
--max-count Maximum number/percentage of counts to keep an taxa [values between 0-1 for percentage, >1
specific number] (default: 0)
--names [ ...] Show only entries matching exact names of the provided list (default: [])
--names-with [ ...] Show entries containing full or partial names of the provided list (default: [])
--taxids [ ...] One or more taxids to report (including children taxa) (default: [])