S

    galah analyse

    Determines the MIMAG quality score for each genome based on completeness, contamination, rRNA gene presence, and tRNA diversity. Supports bacteria, archaea, and eukaryotes.

    By default, galah runs isiteuk to classify each genome into its biological domain (Bacteria, Archaea, or Eukaryota), then selects the appropriate quality tool and marker gene search mode for that domain:

    • Bacteria / Archaea: completeness and contamination estimated by CheckM2; rRNA genes found by Barrnap in bacterial/archaeal mode; tRNAs found by tRNAscan-SE in bacterial/archaeal mode.
    • Eukaryota: completeness and contamination estimated by EukCC; rRNA genes found by Barrnap in eukaryotic mode (finds 18S, 28S, 5.8S, 5S); tRNAs found by tRNAscan-SE in eukaryotic mode. If EukCC cannot estimate quality (e.g. no placement marker genes are found), completeness and contamination are recorded as 0.
    # Classify genomes by domain automatically with isiteuk (default), then run the appropriate tools
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd \
ISITEUK_METAPACKAGE_PATH=/path/to/isiteuk.smpkg \
galah analyse \
    --genome-fasta-files genome1.fna genome2.fna \
    --output-mimag-summary mimag_summary.tsv

# Treat all genomes as bacteria (skips isiteuk; useful when domain is known)
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd \
galah analyse \
    --genome-fasta-files genome1.fna genome2.fna \
    --domain-choice bac \
    --output-mimag-summary mimag_summary.tsv

# Treat all genomes as eukaryotes
EUKCC2_DB=/path/to/eukcc2_db_ver_1.1 \
galah analyse \
    --genome-fasta-files euk1.fna euk2.fna \
    --domain-choice euk \
    --output-mimag-summary mimag_summary.tsv

# Mixed set: isiteuk classifies automatically; provide pre-computed EukCC report to skip EukCC run
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd \
ISITEUK_METAPACKAGE_PATH=/path/to/isiteuk.smpkg \
galah analyse \
    --genome-fasta-files bacteria.fna archaea.fna euk.fna \
    --eukcc-quality-report eukcc_quality.tsv \
    --output-mimag-summary mimag_summary.tsv

# Use a pre-computed isiteuk classification result (avoids re-running isiteuk)
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd \
galah analyse \
    --genome-fasta-files genome1.fna genome2.fna \
    --isiteuk-output isiteuk_results.tsv \
    --output-mimag-summary mimag_summary.tsv

# Use a CheckM2 database specified by argument instead of environment variable
galah analyse \
    --genome-fasta-directory input_genomes/ \
    --domain-choice bac \
    --checkm2-db-path /path/to/checkm2_db.dmnd \
    --output-mimag-summary mimag_summary.tsv

# Use pre-computed CheckM2, Barrnap, and tRNAscan-SE results
galah analyse \
    --genome-fasta-list genomes.txt \
    --domain-choice bac \
    --checkm2-quality-report quality_report.tsv \
    --barrnap-gff-list barrnap_gff_list.tsv \
    --trnascan-out-list trnascan_out_list.tsv \
    --output-mimag-summary mimag_summary.tsv

# Save intermediate outputs to a directory; re-running reuses completed steps
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd \
ISITEUK_METAPACKAGE_PATH=/path/to/isiteuk.smpkg \
galah analyse \
    --genome-fasta-list genomes.txt \
    --working-dir work/ \
    --output-mimag-summary mimag_summary.tsv

    Domain choice

    The --domain-choice flag controls how galah determines the biological domain for each genome:

    ValueDescription
    isiteuk (default)Run isiteuk to classify each genome automatically
    bacTreat all genomes as Bacteria
    arcTreat all genomes as Archaea
    eukTreat all genomes as Eukaryota
    completenessRun CheckM2 and EukCC on every genome and keep whichever reports the higher completeness as a single row
    allRun CheckM2 and EukCC on every genome and report all three domains as separate rows

    Output format

    The --output-mimag-summary TSV contains one row per genome with these columns:

    ColumnDescription
    genomePath to the genome FASTA file
    domainAssigned domain (Bacteria, Archaea, or Eukaryota)
    completenessCompleteness estimate (%)
    contaminationContamination estimate (%)
    rRNA_5SNumber of 5S rRNA genes found
    rRNA_16SNumber of 16S rRNA genes found
    rRNA_23SNumber of 23S rRNA genes found
    rRNA_18SNumber of 18S rRNA genes found (eukaryotes)
    rRNA_28SNumber of 28S rRNA genes found (eukaryotes)
    rRNA_5.8SNumber of 5.8S rRNA genes found (eukaryotes)
    tRNAsNumber of unique standard tRNA types found
    MIMAG_qualityMIMAG quality tier: High quality, Medium quality, or Low quality
    notesEmpty unless the domain call was ambiguous; otherwise records which tools/domains were involved and how the ambiguity was resolved

    MIMAG quality criteria

    Bacteria / Archaea:

    TierCriteria
    High qualityCompleteness ≥ 90%, contamination < 5%, ≥ 1 each of 5S/16S/23S rRNA, ≥ 18 tRNA types
    Medium qualityCompleteness ≥ 50%, contamination < 10% (and not High quality)
    Low qualityCompleteness < 50% or contamination ≥ 10%

    Eukaryota:

    TierCriteria
    High qualityCompleteness ≥ 90%, contamination < 5%, ≥ 1 eukaryotic rRNA (18S/28S/5.8S/5S), ≥ 18 tRNA types
    Medium qualityCompleteness ≥ 50%, contamination < 10% (and not High quality)
    Low qualityCompleteness < 50% or contamination ≥ 10%

    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.

    DOMAIN PARAMETERS

    --domain-choice CHOICE

    Method for determining genome domain. 'isiteuk' runs isiteuk to classify each genome (default). 'bac', 'arc', 'euk' fix all genomes to that domain. 'completeness' runs CheckM2 and EukCC (and matching rRNA/tRNA) for every genome and reports only the higher-completeness domain's result, one row per genome. 'all' runs CheckM2 and EukCC for every genome and reports all three domains as separate rows. [default: isiteuk]

    --isiteuk-output FILE

    Pre-computed isiteuk output TSV. If given, skips running isiteuk when --domain-choice isiteuk.

    --isiteuk-metapackage PATH

    Path to isiteuk metapackage. If not given, uses ISITEUK_METAPACKAGE_PATH environment variable.

    --isiteuk-bacteria-cutoff FLOAT

    Minimum isiteuk num_in_target_domain for Bacteria domain assignment. [default: 10]

    --isiteuk-archaea-cutoff FLOAT

    Minimum isiteuk num_in_target_domain for Archaea domain assignment. [default: 10]

    --isiteuk-eukaryota-cutoff FLOAT

    Minimum isiteuk num_in_target_domain for Eukaryota domain assignment. [default: 20]

    --eukcc-db-path PATH

    Path to EukCC database (required for eukaryotic quality assessment). If not given, uses EUKCC2_DB environment variable.

    --eukcc-quality-report FILE

    Pre-computed merged EukCC TSV with fasta/completeness/contamination columns. If given, skips running EukCC for eukaryotic genomes.

    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

    0

    Successful program execution.

    1

    Unsuccessful program execution.

    101

    The program panicked.

    AUTHOR

    Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>

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