Description

Identify mobile genetic elements present in genomic assemblies

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

FASTA file containing contigs/scaffolds/chromosomes

*.{fasta,fna,fa}

genomad_db (directory)

Directory pointing to geNomad database

score_calibration (boolean)

true/false value to indicate if score calibration should be enabled

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

aggregated_classification (file)

Combined classification scores for each contig/scaffold/chromosome

*_aggregated_classification.tsv

taxonomy (file)

Detailed output of geNomad’s marker gene taxonomy analysis

*_taxonomy.tsv

provirus (file)

Detailed output of each provirus identified by geNomad’s find_proviruses module

*_provirus.tsv

compositions (file)

OPTIONAL - Predicted sample composition when --enable-score-calibration is used

*_compositions.tsv

calibrated_classification (file)

OPTIONAL - Classification scores that have been adjusted based on sample composition when --enable-score-calibration is used`

*_calibrated_aggregated_classification.tsv

plasmid_fasta (file)

FASTA file containing predicted plasmid sequences

*_plasmid.fna

plasmid_genes (file)

TSV file containing predicted plasmid genes and their annotations

*_plasmid_genes.tsv

plasmid_proteins (file)

FASTA file containing predicted plasmid protein sequences

*_plasmid_proteins.faa

plasmid_summary (file)

TSV file containing a summary of geNomad’s plasmid predictions

*_plasmid_summary.tsv

virus_fasta (file)

FASTA file containing predicted virus sequences

*_virus.fna

virus_genes (file)

TSV file containing predicted virus genes and their annotations

*_virus_genes.tsv

virus_proteins (file)

FASTA file containing predicted virus protein sequences

*_virus_proteins.faa

virus_summary (file)

TSV file containing a summary of geNomad’s virus predictions

*_virus_summary.tsv

versions (file)

File containing software versions

versions.yml
included in
phageannotator
author
Github user CarsonJM
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Tools

genomad
Lawrence Berkeley National Labs BSD variant license

Identification of mobile genetic elements

portal.nersc.gov/genomad https://github.com/apcamargo/genomad/ 10.1101/2023.03.05.531206