geNomad v1.5.2

Added

• Display a progress bar showing the progress of the classification process in nn-classification.

Changed

• Update README.md to the database version 1.3.0.

Fixed

• Make mmseqs convertalis output the whole sequence header instead of gene accesions. This prevents parsing conflits with geNomad's other components in cases where MMseqs2 uses its built-in special parsers for specific header formats (e.g. RefSeq).

geNomad v1.5.1

Added

• Add the --threads parameter to the nn-classification module, which allows controlling the number of threads used for classifying sequences using the neural network model.

Changed

• Mention post-classification filters the in the summary module description.

geNomad v1.5.0

Changed

• Given that geNomad applies a minimum score filter (since version 1.4.0), the help dialogue of the --min-score parameter was modified to remove the following sentence: "By default, the sequence is classified as virus/plasmid if its virus/plasmid score is higher than its chromosome score, regardless of the value".
• The following parameters were added to the MMseqs2 search command: --max-seqs 1000000 --min-ungapped-score 20 --max-rejected 225. As a result, changing --splits won't affect the search results anymore. Thanks @milot-mirdita.

geNomad v1.4.0

Added

• Mention Docker and the NMDC EDGE implementation in the README.md.
• Add the --min-plasmid-hallmarks-short-seqs and --min-virus-hallmarks-short-seqs parameters. These options allow filtering out short sequences (less than 2,500 bp) that don't encode a minimum number of hallmark genes. By default, short sequences need to encode at least one hallmark to be classified as a virus or a plasmid.
• Add the --conservative and --relaxed presets that control post-classification filters. The --conservative option makes those filters even more aggressive, resulting in more restricted sets of plasmid and virus, containing only sequences whose classification is strongly supported. The --relaxed preset disables all post-classification filters.

Changed

• Windows with more than 4,000 Ns are ignored when encoding sequences for the neural network classification. The first window is always processed, regardless of the amount of Ns.
• Changed the default value of --min-score from 0.0 to 0.7.
• Changed the default search sensitivity from 4.0 to 4.2.
• Update README.md to version 1.4.0. This includes mentions to the --conservative and --relaxed flags and a warning about how changes in --splits can affect geNomad's output.

geNomad v1.3.3

Fixed

• Fix a bug in score-calibration that happened when find-proviruses was executed but no provirus was detected. The module now checks if proviruses were detected (using utils.check_provirus_execution) before counting the total number of sequences.

geNomad v1.3.2

Fixed

• Require numpy <1.6. Fixes #7, which occurs because numba doesn't support numpy >=1.24 yet.

geNomad v1.3.1

Fixed

• Check if find-proviruses was executed when counting the number of sequences in the score-calibration module (thanks Spencer Diamond for pointing this error out!).

geNomad v1.3.0

Added

• Add support for AMR annotation.
• Update database parsing to allow BUSCO-based USCGs.

Changed

• Sequences with no terminal repeats will be flagged with No terminal repeats, as Linear can be misleading.
• Print the number of plasmids and viruses in the summary module.
• Set click.rich_click.MAX_WIDTH to None.
• Reduce the default --sensitivity to 4.0.
• Update README.md to version 1.3.0.

Fixed

• Set prog_name in click.version_option.

geNomad v1.2.0

Changed

• Mention the Zenodo upload of geNomad's database in README.md.
• Add the following sentence for the help dialogue of the --min-plasmid-marker-enrichment, --min-virus-marker-enrichment, --min-plasmid-hallmarks, and --min-virus-hallmarks parameters: "This option will be ignored if the annotation module was not executed".
• Apply a uniform prior to the empirical sample composition in score_batch_correction. This will shrink the effect of calibration when the empirical composition distribution is very skewed.
• Reduce the --min-score in the README.md example to 0.7.

Fixed

• Fix a bug in the score calibration module where the sample size was set to a constant value and the "Your sample has less than 1,000 sequences…" warning would always appear.

geNomad v1.1.0

Added

• Dockerfile for version 1.0.0.
• Sequence class: add support for str in __eq__.
• Sequence class: add a __hash__ method.
• Compute marker enrichment in the marker-classification module.
• Add columns for plasmid and virus marker enrichment to the _plasmid_summary.tsv and _virus_summary.tsv files.
• Set --min-plasmid-marker-enrichment and --min-virus-marker-enrichment to 0 as default. This will alter the results when using default parameters.
• Add support for plasmid and virus hallmarks. Requires geNomad database v1.1.
• Add CONJscan annotations to _plasmid_summary.tsv. Requires geNomad database v1.1.

Changed

• Sequence class: simplify has_dtr return statement.
• Sequence class: make __repr__ more friendly for long sequences.
• Sequence class: rename the id property to accession.
• Amino acids are now written to _provirus_aragorn.tsv.
• Update the XGBoost model file to the .ubj format.
• Require xgboost >=1.6.
• The taxonomic lineage in _taxonomy.tsv and _virus_summary.tsv will use Viruses as the highest rank, instead of root.
• Change order of the columns in _plasmid_summary.tsv and _virus_summary.tsv.
• Explicitly set fraction to 0.5 in taxopy.find_majority_vote.

Fixed

• tRNA coordinates are now 1-indexed.
• Write summary_execution_info.
• Fix a problem in DatabaseDownloader.get_version where only the major version was compared.