singlem supplement

DESCRIPTION

Create a new metapackage from a vanilla one plus new genomes

OPTIONS

--new-genome-fasta-files NEW_GENOME_FASTA_FILES [NEW_GENOME_FASTA_FILES ...]

FASTA files of new genomes

--new-genome-fasta-files-list NEW_GENOME_FASTA_FILES_LIST [NEW_GENOME_FASTA_FILES_LIST ...]

File containing FASTA file paths of new genomes

--input-metapackage INPUT_METAPACKAGE

metapackage to build upon [default: Use default package]

--output-metapackage OUTPUT_METAPACKAGE

output metapackage

--threads THREADS

parallelisation

TAXONOMY

--new-fully-defined-taxonomies NEW_FULLY_DEFINED_TAXONOMIES

newline separated file containing taxonomies of new genomes (path<TAB>taxonomy). Must be fully specified to species level. If not specified, the taxonomy will be inferred from the new genomes using GTDB-tk or read from --taxonomy-file [default: not set, run GTDBtk].

--taxonomy-file TAXONOMY_FILE

A 2 column tab-separated file containing each genome's taxonomy as output by GTDBtk [default: not set, run GTDBtk]

--gtdbtk-output-directory GTDBTK_OUTPUT_DIRECTORY

use this GTDBtk result. Not used if --new-taxonomies is used [default: not set, run GTDBtk]

--pplacer-threads PPLACER_THREADS

for GTDBtk classify_wf

--output-taxonomies OUTPUT_TAXONOMIES

TSV output file of taxonomies of new genomes, whether they are novel species or not.

--skip-taxonomy-check

skip check which ensures that GTDBtk assigned taxonomies are concordant with the old metapackage's [default: do the check]

QUALITY FILTERING OF NEW GENOMES

--checkm2-quality-file CHECKM2_QUALITY_FILE

CheckM2 quality file of new genomes

--no-quality-filter

skip quality filtering

--checkm2-min-completeness CHECKM2_MIN_COMPLETENESS

minimum completeness for CheckM2 [default: 50]

--checkm2-max-contamination CHECKM2_MAX_CONTAMINATION

maximum contamination for CheckM2 [default: 10]

DEREPLICATION

--no-dereplication

Assume genome inputs are already dereplicated

--dereplicate-with-galah

Run galah to dereplicate genomes at species level

LESS COMMON OPTIONS

--hmmsearch-evalue HMMSEARCH_EVALUE

evalue for hmmsearch run on proteins to gather markers [default: 1e-20]

--gene-definitions GENE_DEFINITIONS

Tab-separated file of genome_fasta<TAB>transcript_fasta<TAB>protein_fasta [default: undefined, call genes using Prodigal]

--working-directory WORKING_DIRECTORY

working directory [default: use a temporary directory]

--no-taxon-genome-lengths

Do not include taxon genome lengths in updated metapackage

--ignore-taxonomy-database-incompatibility

Do not halt when the old metapackage is not the default metapackage.

--new-taxonomy-database-name NEW_TAXONOMY_DATABASE_NAME

Name of the taxonomy database to record in the created metapackage [default: custom_taxonomy_database]

--new-taxonomy-database-version NEW_TAXONOMY_DATABASE_VERSION

Version of the taxonomy database to use [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