GenoChar 0.6.3.2

GenoChar: summarize-first genome characterization workflow with one-time managed setup for Prokka and CheckM2

GenoChar

GenoChar generates publication-ready genome characterization tables for bacterial and archaeal genomes.

Version 0.6.3.2 keeps the single-command, summarize-first interface, but adds a practical solution for external-tool dependency conflicts:

• genochar builds the final genome characterization table
• genochar setup prepares managed Prokka and CheckM2 conda environments under ~/.genochar
• later, a normal genochar ... --check --annotate prokka run automatically calls those managed environments with conda run -p ...

That means users do not need to manually solve a shared Prokka/CheckM2 environment.

The main output is a wide table with one row per strain. Optional outputs include a feature-style table and an Excel workbook.

Naming note: the project/display name is GenoChar, while the Python package name and command-line executable remain lowercase as genochar.

What the tool computes

FASTA-derived fields

These work even if you provide only FASTA files:

• Strain
• Strain name
• Genus
• Species
• Accession
• Genome size (bp)
• GC content (%)
• No. of contigs
• N50 (bp)
• N90 (bp)
• L50
• L90
• Longest contig (bp)
• Gaps (N per 100 kb)

GFF-derived fields

These are added when you provide GFF files or ask GenoChar to create annotation files:

• CDSs
• tRNAs
• rRNAs
• tmRNA
• misc RNA
• Repeat regions
• 16S rRNA count
• 16S rRNA length (bp)
• 16S rRNA contig
• 16S rRNA sequence

CheckM2-derived fields

These are added when you provide or generate a CheckM2 report:

• Completeness (%)
• Contamination (%)

User-supplied metadata

Optional input tables can add:

• Sequencing coverage (×)
• Sequencing platforms
• Assembly method
• Genus
• Species
• Accession
• Repeat regions

Default output columns

The main output table contains:

• Strain
• Strain name
• Genus
• Species
• Accession
• Genome size (bp)
• GC content (%)
• No. of contigs
• N50 (bp)
• N90 (bp)
• L50
• L90
• Longest contig (bp)
• Gaps (N per 100 kb)
• Sequencing coverage (×)
• Sequencing platforms
• Assembly method
• CDSs
• tRNAs
• rRNAs
• tmRNA
• misc RNA
• Repeat regions
• 16S rRNA count
• 16S rRNA length (bp)
• 16S rRNA contig
• 16S rRNA sequence
• Completeness (%)
• Contamination (%)

Installation

Clone the repository and install GenoChar into the active Python environment:

git clone https://github.com/ljunwon1114/GenoChar.git
cd GenoChar
pip install -e .

If you just want the latest GitHub version without cloning for development, you can also use:

pip install git+https://github.com/ljunwon1114/GenoChar.git

Core Python requirement

GenoChar itself is lightweight. The core package now declares:

• requires-python >=3.10

The external tools are the difficult part, so v0.6.3.2 no longer assumes that Prokka and CheckM2 should share the same environment.

One-time managed setup (recommended)

Run this once:

genochar setup

This creates managed environments under ~/.genochar, typically:

~/.genochar/
  config.json
  envs/
    prokka/
    checkm2/
  databases/
    CheckM2_database/

After that, normal workflow commands automatically use those managed environments when --annotate prokka and/or --check are requested.

When --check is used, GenoChar now passes the resolved input FASTA files directly to checkm2 predict --input ..., matching the official CheckM2 interface that accepts either a folder of bins or a list of FASTA files.

Reuse an existing CheckM2 database

If you already downloaded the CheckM2 database, point setup at it directly:

genochar setup --checkm2-db /home/jwlee/databases/CheckM2_database/uniref100.KO.1.dmnd

You can also pass a directory that contains the .dmnd file.

Optional setup flags

genochar setup --skip-prokka
genochar setup --skip-checkm2
genochar setup --force

• --skip-prokka: only prepare CheckM2
• --skip-checkm2: only prepare Prokka
• --force: recreate managed environments even if they already exist

Command overview

A. FASTA only

genochar -i "assemblies/*.fasta" -o genome_characterization.tsv

B. FASTA + existing GFF + existing CheckM2 report

genochar -i "assemblies/*.fasta" --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv

C. FASTA + managed CheckM2 first + managed Prokka annotation

genochar -i "assemblies/*.fasta" --check --annotate prokka -k Archaea -t 8 -w genochar_work -o genome_characterization.tsv

D. Reuse existing GFF files automatically

genochar -i "assemblies/*.fasta" --annotate existing --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv

E. Reuse explicitly supplied GFF files in existing-annotation mode

genochar -i "assemblies/*.fasta" --annotate existing --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv

Optional extra outputs

Feature-style table

genochar -i "assemblies/*.fasta" -f genome_characterization_feature.tsv -o genome_characterization.tsv

Excel workbook

genochar -i "assemblies/*.fasta" -x genome_characterization.xlsx -o genome_characterization.tsv

Coverage input

Coverage cannot be derived from FASTA alone. If you want to fill Sequencing coverage (×), provide a coverage table.

Example:

Strain	Coverage
IOH03	55.7
IOH05	50.3

or

Strain	Total bases
IOH03	110.8 Mbp
IOH05	107.6 Mbp

If Total bases is provided, GenoChar computes:

Sequencing coverage (×) = Total bases / Genome size

Metadata input

Optional metadata columns include:

• Strain
• Sequencing platforms
• Assembly method
• Genus
• Species
• Accession
• Repeat regions
• Sequencing coverage (×)

Example:

Strain	Genus	Species	Accession	Sequencing platforms	Assembly method
IOH03	Thermococcus	waiotapuensis	GCF_032304395	Illumina iSeq 100	Unicycler (short-read assembly)
IOH05	Thermococcus	sp.	GCA_000000000	Illumina iSeq 100	Unicycler (short-read assembly)

Notes

• GenoChar is summarize-first by default. If you only pass FASTA, GFF, CheckM2, coverage, and metadata inputs, it behaves like a direct summarization tool.
• genochar setup is the recommended way to prepare Prokka and CheckM2 without forcing them into one shared environment.
• --annotate prokka tells GenoChar to create annotation files before building the final table.
• --annotate existing tells GenoChar to reuse nearby GFF files or explicitly supplied --gff inputs.
• --check runs CheckM2 internally before annotation and automatically integrates the resulting quality_report.tsv into the final table.
• --check-report reuses an existing CheckM2 quality_report.tsv file.
• --check and --check-report are mutually exclusive.
• --gff is intended for existing annotation files and should not be combined with --annotate prokka.
• If more than one 16S rRNA feature is found, GenoChar stores the longest 16S sequence in the main table.
• Legacy genochar summarize ... and genochar pipeline ... calls are still accepted in v0.6.3, but the preferred interface is the single-command form shown above.

License

MIT