galah analyse

Determines the MIMAG quality score based on completeness, contamination, rRNA, and tRNA presence. Completeness and contamination are estimated using CheckM2 by default, unless CheckM1/2 quality reports are provided.

# Example: determine MIMAG quality scores
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd galah analyse --genome-fasta-files genome1.fna genome2.fna --output-mimag-summary mimag.tsv
# Example: determine MIMAG quality scores for a directory of genomes using CheckM2 database specified by argument
galah analyse --genome-fasta-directory input_genomes/ --checkm2-db-path /path/to/checkm2_db.dmnd --output-mimag-summary mimag_summary.tsv
# Example: determine MIMAG quality scores using precomputed CheckM2, Barrnap, and tRNASCAN-SE results
galah analyse --genome-fasta-list genomes.txt --output-mimag-summary mimag_summary.tsv \
    --checkm2-quality-report quality_report.tsv --barrnap-gff-list barrnap_gff_list.tsv --trnascan-out-list trnascan_out_list.tsv

GENOME INPUT

-f, --genome-fasta-files PATH ..

Path(s) to FASTA files of each genome e.g. pathA/genome1.fna pathB/genome2.fa.

-d, --genome-fasta-directory PATH

Directory containing FASTA files of each genome.

-x, --genome-fasta-extension EXT

File extension of genomes in the directory specified with -d/--genome-fasta-directory. [default: fna]

--genome-fasta-list PATH

File containing FASTA file paths, one per line.

QUALITY PARAMETERS

--quality-method NAME

method for finding genome quality. 'checkm2' for CheckM2. [default: checkm2]

--checkm2-db-path PATH

Path to CheckM2 database (required for CheckM2 quality method). If not given, will use CHECKM2DB environment variable if set.

--checkm2-quality-report PATH

Path to pre-generated CheckM2 quality_report.tsv file. If given, will use this file instead of running quality method.

--checkm-tab-table PATH

Path to pre-generated CheckM tab table file. If given, will use this file instead of running quality method.

RNA PARAMETERS

--rrna-method NAME

method for finding rRNA genes. 'barrnap' for Barrnap. [default: barrnap]

--trna-method NAME

method for finding tRNA genes. 'trnascan' for tRNAscan-SE. [default: trnascan]

--barrnap-gff-list PATH

Path to two-column TSV file mapping genome paths (as given in input) to Barrnap GFF paths (no headers). If given, will use these files instead of running rRNA method.

--trnascan-out-list PATH

Path to two-column TSV file mapping genome paths (as given in input) to tRNAscan-SE output paths (no headers). If given, will use these files instead of running tRNA method.

OUTPUT

--output-mimag-summary PATH

Output a tsv file summarising the MIMAG status for each genome.

--output-quality-report PATH

Output a CheckM2-format quality report TSV file.

GENERAL PARAMETERS

-t, --threads INT

Number of threads. [default: 1]

-v, --verbose

Print extra debugging information

-q, --quiet

Unless there is an error, do not print log messages

-h, --help

Output a short usage message.

--full-help

Output a full help message and display in 'man'.

--full-help-roff

Output a full help message in raw ROFF format for conversion to other formats.

EXIT STATUS

Successful program execution.

Unsuccessful program execution.

101

The program panicked.

AUTHOR

Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology

Galah