apcamargo/genomad: geNomad v1.1.0

Published August 23, 2022 | Version v1.1.0

Software Open

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 it only only compared the major version.

Files

Name	Size	Download all
apcamargo/genomad-v1.1.0.zip md5:5f383967a469e2451443c10dad827402	26.6 MB	Preview Download