Usage¶

Warning

Only the GTDB_refseq@2.0.0 collection is supported at present. MetaPanG rejects an unsupported collection@version, and a few species are discarded by default within a supported release (see Collection compatibility).

profile is the main command. Around it, list and cache browse and manage the pangenome data a run needs, and the search commands expose the matching steps profile performs internally. Run metapang --help to see every command.

Global options¶

A few options belong to the top-level metapang command rather than to a subcommand, so they are given before the command name:

metapang [GLOBAL OPTIONS] COMMAND [COMMAND OPTIONS]

Option	Default	Description
`-v`, `--verbosity`	`info`	Log verbosity, one of `trace`, `debug`, `info`, `warning`, `error`, `critical`.
`-c`, `--config`		Path to a configuration file for this run (see Configuration).
`-l`, `--log-file`		Also write the log to this file.
`--version`		Show the `MetaPanG` version and exit.
`--help`		Show help and exit. Works on any command, for example `metapang profile --help`.

# more verbose profiling
metapang -v debug profile reads.fastq.gz -b GTDB_refseq@2.0.0

# use a specific configuration file
metapang -c config.toml profile reads.fastq.gz -b GTDB_refseq@2.0.0

# combine global options
metapang -v debug -l run.log profile reads.fastq.gz -b GTDB_refseq@2.0.0

Note

Putting these after the command, for example metapang profile -v debug ..., is an error: -v, -c, and -l are options of metapang, not of profile.

metapang list, metapang cache: Browse the PanGBank catalog and manage the locally cached data, including pre-downloading a collection before a run. See Managing pangenome data.
metapang profile: The main command. Given metagenomic reads and a pangenome collection, it detects the species present, maps the reads onto each species pangenome, and resolves the mixture of strains with their abundances and gene content. See metapang profile.
metapang search bank: Match a query (a genome or reads) against a whole collection to find which genomes and pangenomes it resembles. This is the species-detection step, on its own. See metapang search bank.
metapang search pangenome: Match a query against a single species pangenome de Bruijn graph to find which gene families it contains, using exact k-mer lookup. See metapang search pangenome.