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
<p><b>Copyright information:</b></p><p>Taken from "Optimization of filtering criterion for SEQUEST d...
The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding va...
What's Changed Update README.md by @MMedzin in https://github.com/MMedzin/clustering-genomic-data/p...
Changed Mention the Zenodo upload of geNomad's database in README.md. Add the following sentence fo...
Added Mention Docker and the NMDC EDGE implementation in the README.md. Add the --min-plasmid-hallm...
Fixed Fix a bug in score-calibration that happened when find-proviruses was executed but no proviru...
Fixed Check if find-proviruses was executed when counting the number of sequences in the score-cali...
Added Dockerfile for version 1.0.0. Sequence class: add support for str in __eq__. Sequence class: ...
Added Display a progress bar showing the progress of the classification process in nn-classificatio...
Marker database used by geNomad for virus and plasmid identification. genomad_db_v1.0.tar.gz: MMs...
Bugfix --min-cov now filters unique transcripts from coverage, mismatch, readthrough and stop table...
Changes since 1-c7a89 Release New Features Translated searches (blastx and tblastn like search mode...
New Taxonomy Workflow (new feature and breaking change) We introduce a new taxonomy workflow for ass...
updated filtering so alignments within minimum length of start and end of genome use query target - ...
<p>Shown are the sequence-based score (x-axis) for 273 stop-gain variants reported by the ESP and 10...
<p><b>Copyright information:</b></p><p>Taken from "Optimization of filtering criterion for SEQUEST d...
The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding va...
What's Changed Update README.md by @MMedzin in https://github.com/MMedzin/clustering-genomic-data/p...
Changed Mention the Zenodo upload of geNomad's database in README.md. Add the following sentence fo...
Added Mention Docker and the NMDC EDGE implementation in the README.md. Add the --min-plasmid-hallm...
Fixed Fix a bug in score-calibration that happened when find-proviruses was executed but no proviru...
Fixed Check if find-proviruses was executed when counting the number of sequences in the score-cali...
Added Dockerfile for version 1.0.0. Sequence class: add support for str in __eq__. Sequence class: ...
Added Display a progress bar showing the progress of the classification process in nn-classificatio...
Marker database used by geNomad for virus and plasmid identification. genomad_db_v1.0.tar.gz: MMs...
Bugfix --min-cov now filters unique transcripts from coverage, mismatch, readthrough and stop table...
Changes since 1-c7a89 Release New Features Translated searches (blastx and tblastn like search mode...
New Taxonomy Workflow (new feature and breaking change) We introduce a new taxonomy workflow for ass...
updated filtering so alignments within minimum length of start and end of genome use query target - ...
<p>Shown are the sequence-based score (x-axis) for 273 stop-gain variants reported by the ESP and 10...
<p><b>Copyright information:</b></p><p>Taken from "Optimization of filtering criterion for SEQUEST d...
The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding va...
What's Changed Update README.md by @MMedzin in https://github.com/MMedzin/clustering-genomic-data/p...