singlem regenerate

DESCRIPTION

Update a SingleM package with new sequences and taxonomy (expert mode).

OPTIONS

--min-aligned-percent percent

remove sequences from the alignment which do not cover this percentage of the HMM [default: 10]

--window-position WINDOW_POSITION

change window position of output package [default: do not change]

--sequence-prefix SEQUENCE_PREFIX

add a prefix to sequence names

--candidate-decoy-sequences, --euk-sequences CANDIDATE_DECOY_SEQUENCES

candidate amino acid sequences fasta file to search for decoys

--candidate-decoy-taxonomy, --euk-taxonomy CANDIDATE_DECOY_TAXONOMY

tab-separated sequence ID to taxonomy file of candidate decoy sequences

--no-candidate-decoy-sequences, --no-further-euks

Do not include any euk sequences beyond what is already in the current SingleM package

REQUIRED ARGUMENTS

--input-singlem-package PATH

input package path

--output-singlem-package PATH

output package path

--input-sequences INPUT_SEQUENCES

all on-target amino acid sequences fasta file for new package

--input-taxonomy INPUT_TAXONOMY

tab-separated sequence ID to taxonomy file of on-target sequence taxonomy

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