Overview
- Hashed cgMLST
- Clustering functionality and interface for minimum-spanning-trees
- Antimicrobial Resistance Screening with NCBI/AMRFinder
- Robustified allelic typing
- Improvements in user interface
- Option to save assembly files to local database
- Various bugfixes
- and more ...
To install this update follow the instructions given in README - 2 Installation.
Release 1.5.0 contains substantial improvements, novelties, fixes and other changes. Most notable is the introduction of hashed cgMLST. Allele sequences are now hashed by default using SHA-256. Upon download of a cgMLST scheme, all alleles respectively belonging to the loci included in the scheme are hashed, with the resulting unique 64-bit words substituting numeric sequence indexes. This change allows efficient and robust comparison of results from collaborating working groups. PhyloTrace is aiming to become universally compatible - a goal only achievable using hashing technology. This fundament is now integrated and will be enriched with more utility in upcoming releases.
Another milestone is the introduction of Antimicrobial Resistance Screening with AMRFinder/NCBI. The new "Gene Screening" interface allows to query the isolates present in the local database for resistance, virulence, stress genes and more. For now, the results are saved to the database and can be inspected and exported. In future users will be able to visualize this information.
Minimum-spanning tree (MST) network graphs were supplemented with a cluster feature - an ability crucial for isolate comparison. Users can choose between "Area" and "Skeleton" cluster types, both visualizing isolates clustering with each other according to a customizable threshold. Next to these major changes, version 1.5.0 contains numerous improvements regarding user experience, interface and robustness.
Note, that due to these significant changes, PhyloTrace 1.5.0 is not backwards-compatible with previous versions. Local databases need to be completely reconstructed.
