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)
Data used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by ...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
This zip package includes the annotated genbank files (affiliation against PFAM and Refseq) of all v...
Added Dockerfile for version 1.0.0. Sequence class: add support for str in __eq__. Sequence class: ...
Added Add support for AMR annotation. Update database parsing to allow BUSCO-based USCGs. Changed ...
Added Mention Docker and the NMDC EDGE implementation in the README.md. Add the --min-plasmid-hallm...
Changed Mention the Zenodo upload of geNomad's database in README.md. Add the following sentence fo...
Fixed Replace np.warnings with warnings to add compatibility with numpy >= 1.24
Added Display a progress bar showing the progress of the classification process in nn-classificatio...
Fixed Check if find-proviruses was executed when counting the number of sequences in the score-cali...
Marker database used by geNomad for virus and plasmid identification. genomad_db_v1.0.tar.gz: MMs...
Fixed Fix a bug in score-calibration that happened when find-proviruses was executed but no proviru...
Changed structure of some files for better overwiew Fixed an issue with compounds when both parents ...
benchmark_data: Data used to train and evaluate the classification models. giant_virus_data: Sequen...
Identifying and characterizing mobile genetic elements in sequencing data is essential for understan...
Data used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by ...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
This zip package includes the annotated genbank files (affiliation against PFAM and Refseq) of all v...
Added Dockerfile for version 1.0.0. Sequence class: add support for str in __eq__. Sequence class: ...
Added Add support for AMR annotation. Update database parsing to allow BUSCO-based USCGs. Changed ...
Added Mention Docker and the NMDC EDGE implementation in the README.md. Add the --min-plasmid-hallm...
Changed Mention the Zenodo upload of geNomad's database in README.md. Add the following sentence fo...
Fixed Replace np.warnings with warnings to add compatibility with numpy >= 1.24
Added Display a progress bar showing the progress of the classification process in nn-classificatio...
Fixed Check if find-proviruses was executed when counting the number of sequences in the score-cali...
Marker database used by geNomad for virus and plasmid identification. genomad_db_v1.0.tar.gz: MMs...
Fixed Fix a bug in score-calibration that happened when find-proviruses was executed but no proviru...
Changed structure of some files for better overwiew Fixed an issue with compounds when both parents ...
benchmark_data: Data used to train and evaluate the classification models. giant_virus_data: Sequen...
Identifying and characterizing mobile genetic elements in sequencing data is essential for understan...
Data used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by ...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
This zip package includes the annotated genbank files (affiliation against PFAM and Refseq) of all v...