mumu_pq: MUMU reclustering of class 'physeq'

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

MUMU reclustering of class physeq

Description

See https://www.nature.com/articles/s41467-017-01312-x for more information on the original method LULU. This is a wrapper of mumu a C++ re-implementation of LULU by Frédéric Mahé

Usage

mumu_pq(
  physeq,
  nproc = 1,
  id = 0.84,
  vsearchpath = find_vsearch(),
  mumupath = "mumu",
  lulu_exact = FALSE,
  verbose = FALSE,
  clean_pq = TRUE,
  keep_temporary_files = FALSE,
  extra_mumu_args = NULL
)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
nproc	(default 1) Set to number of cpus/processors to use for the clustering
id	(default: 0.84) id for –usearch_global.
vsearchpath	(default: vsearch) path to vsearch.
mumupath	path to mumu. See mumu for installation instruction
lulu_exact	(logical) If true, use the exact same algorithm as LULU corresponding to the –legacy option of mumu. Need mumu version >= v1.1.0
verbose	(logical) If true, print some additional messages.
clean_pq	(logical) If true, empty samples and empty ASV are discarded before clustering.
keep_temporary_files	(logical, default: FALSE) Do we keep temporary files
extra_mumu_args	(character, default: NULL) Additional arguments passed on to mumu command line. See ⁠man mumu⁠ into bash for details. Major args are --minimum_match, --minimum_ratio_type, --minimum_ratio, --minimum_relative_cooccurence and --threads

Details

This function is mainly a wrapper of the work of others. Please cite mumu and lulu if you use this function for your work.

Value

a list of for object

• "new_physeq": The new phyloseq object (class physeq)

• "mumu_results": The log file of the mumu software. Run ⁠man mumu⁠ into bash to obtain details about columns' signification.

Author(s)

Frédéric Mahé & Adrien Taudière [e-mail]

References

• MUMU: https://github.com/frederic-mahe/mumu

• VSEARCH can be downloaded from https://github.com/torognes/vsearch.

See Also

lulu_pq()

Examples

## Not run: 
ntaxa(data_fungi_sp_known)
ntaxa(mumu_pq(data_fungi_sp_known)$new_physeq)
ntaxa(mumu_pq(data_fungi_sp_known, extra_mumu_args = "--minimum_match 90")$new_physeq)

## End(Not run)

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.