singlem condense

DESCRIPTION

Combine OTU tables across different markers into a single taxonomic profile. Note that while this mode can be run independently, it is often more straightforward to invoke its methodology by specifying -p / --taxonomic- profile when running pipe mode.

OPTIONS

INPUT ARGUMENTS (1+ REQUIRED)

--input-archive-otu-tables, --input-archive-otu-table INPUT_ARCHIVE_OTU_TABLES [INPUT_ARCHIVE_OTU_TABLES ...]

Condense from these archive tables

--input-archive-otu-table-list INPUT_ARCHIVE_OTU_TABLE_LIST

Condense from the archive tables newline separated in this file

--input-gzip-archive-otu-table-list INPUT_GZIP_ARCHIVE_OTU_TABLE_LIST

Condense from the gzip'd archive tables newline separated in this file

OUTPUT ARGUMENTS (1+ REQUIRED)

-p, --taxonomic-profile filename

output OTU table

--taxonomic-profile-krona filename

name of krona file to generate.

--output-after-em-otu-table filename

output OTU table after expectation maximisation has been applied. Note that this table usually contains multiple rows with the same window sequence.

OTHER OPTIONS

--metapackage METAPACKAGE

Set of SingleM packages to use [default: use the default set]

--min-taxon-coverage FRACTION

Set taxons with less coverage to coverage=0. [default: 0.35]

--trim-percent TRIM_PERCENT

percentage of markers to be trimmed for each taxonomy [default: 10]

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