geNomad v1.8.0

Added

• Added the --min-number-genes parameter to the summary module. This parameter allows users to set the minimum number of genes a sequence must encode to be considered for classification as a plasmid or virus. The default value is 1. When --conservative is used, this parameter is set to 1. When --relaxed is used, this parameter is set to 0. This filter has no effect if the annotate module is not executed.

Changed

• Added a hyperlink to the official documentation in the help dialogue.
• The virus taxonomic lineage is presented using a fixed number of fields separated by semicolons (;). As a result, for genomes that could not be assigned to the family level (the most specific taxonomic rank), there will be trailing semicolons at the end of the lineage string.
• Do not apply the gene-based post-classification filters when the annotate module is not executed.
• Set the default value of --min-plasmid-marker-enrichment to 0.1.

geNomad v1.7.6

Fixed

• Set maximum keras version to below 3.0. This prevents errors due to incompatibility with keras >=3.0, such as the shape parameter not accepting an integer as input.

geNomad v1.7.5

Fixed

• Set the CUDA_VISIBLE_DEVICES environment variable to -1 in nn_classification. This fixes a bug where the nn_classification module would fail to run when a GPU was available and the input had a single sequence.

geNomad v1.7.4

Fixed

• Fixed the parsing of MMseqs2 integrase output to extract only the gene accession, rather than the entire header. This addresses a bug introduced in version 1.5.2, where the integrase gene accession was not accurately parsed because the entire header was extracted. As a result, the find-proviruses module can now properly add integrases to gene tables and extend boundaries using integrase coordinates.

Changed

• Replace ambiguous variable name in read_fasta.
• Define name current_contig at the beginning of _append_aragorn_tsv.

geNomad v1.7.3

Fixed

• Set minimum pyrodigal-gv version to 0.3.1. This fixes a bug introduced in 0.3.0 that led to the identification of RBS motifs not reported by Prodigal.

Changed

• Remove the CCGGGG RBS motif from the list of motifs.

geNomad v1.7.2

Fixed

• Add the CCGGGG RBS motif to the list of motifs.

Changed

• Do not include stop codon (*) at the end of protein sequences.
• Set minimum pyrodigal-gv version to 0.2.0.

geNomad v1.7.1

Changed

• Replace prodigal-gv with pyrodigal-gv

geNomad v1.7.0

Changed

• The mmseqs search command has been replaced by a two-step alignment workflow. In the first alignment step, --alignment-mode 1 and --max-rejected are utilized, while the second step uses --alignment-mode 2 and -c 0.2. This change reduces the number of alignments that are rejected due to not meeting the minimum coverage cutoff and mitigates the issue where the annotation results change when the input sequence order is altered.
• The --min-ungapped-score parameter of mmseqs prefilter was increased from 20 to 25.
• The --max-rejected parameter of the first mmseqs align step was increased from 225 to 280.

geNomad v1.6.1

Fixed

• Replace np.warnings with warnings to add compatibility with numpy >= 1.24.

geNomad v1.6.0

Changed

• Update numba (>=0.57) and numpy (>=1.21) version requirements.
• Use casefold for sequence comparison within the Sequence class.
• Remove type annotations of methods of the Sequence class that return an instance of Sequence.
• Use console.status to log the deletion of the .tar.gz file during the execution of download-database.
• Make the conservative assignment at the family level optional via the --conservative-taxonomy parameter. This increases the amount of viral genomes assigned to a family when executing geNomad with default parameters.

Fixed

• Fix parameter names in the error message of --conservative and --relaxed (e.g. --min_score → --min-score).