---
title: Galah analyse
---
# 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.
```bash
# 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
**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>