singlem metapackage

DESCRIPTION

Create or describe a metapackage (i.e. set of SingleM packages)

OPTIONS

--metapackage METAPACKAGE

Path to write generated metapackage to

--singlem-packages SINGLEM_PACKAGES [SINGLEM_PACKAGES ...]

Input packages

--nucleotide-sdb NUCLEOTIDE_SDB

Nucleotide SingleM database for initial assignment pass

--no-nucleotide-sdb

Skip nucleotide SingleM database

--taxon-genome-lengths TAXON_GENOME_LENGTHS

TSV file of genome lengths for each taxon

--no-taxon-genome-lengths

Skip taxon genome lengths

--taxonomy-database-name TAXONOMY_DATABASE_NAME

Name of the taxonomy database to use [default: custom_taxonomy_database]

--taxonomy-database-version TAXONOMY_DATABASE_VERSION

Version of the taxonomy database to use [default: unspecified]

--diamond-prefilter-performance-parameters DIAMOND_PREFILTER_PERFORMANCE_PARAMETERS

Performance-type arguments to use when calling 'diamond blastx' during the prefiltering. [default: '--block-size 0.5 --target-indexed -c1']

--diamond-taxonomy-assignment-performance-parameters DIAMOND_TAXONOMY_ASSIGNMENT_PERFORMANCE_PARAMETERS

Performance-type arguments to use when calling 'diamond blastx' during the taxonomy assignment. [default: '--block-size 0.5 --target-indexed -c1']

--describe

Describe a metapackage rather than create it

--threads num_threads

number of CPUS to use [default: 1]

--prefilter-clustering-threshold fraction

ID for dereplication of prefilter DB [default: 0.6]

--prefilter-diamond-db DMND

Dereplicated DIAMOND db for prefilter to use [default: dereplicate from input SingleM packages]

--makeidx-sensitivity-params PARAMS

DIAMOND sensitivity parameters to use when indexing the prefilter DIAMOND db. [default: None]

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

AUTHORS

Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Samuel Aroney, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
Raphael Eisenhofer, Centre for Evolutionary Hologenomics, University of Copenhagen, Denmark
Rossen Zhao, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology