- Replaced Kraken based kmer taxonomic classification by a Mash lookup / ANI computation approach
- Updated CARD db to 3.0.7
- Updated VFDB to 2020-04-28
- Updated PubMLST to 2020-04-28
- Improved scaffolding runtime performance
- Added JVM shutdown hook to delete tmp directories
- Fixed a memory leak in scaffolding report creation
- Fixed config strain check regex
- Removed redundand QC mapping index files
- Improved the
-c/--checklogic and error messages - Replaced the configuration example by a more versatile one
- Fixed a "permission denied error" in the Docker container
- Added an option to skip characterization/comparative analysis steps
- Enhanced the Docker shell script (asap-docker.sh) (more options, use user:group file ownerships)
- Replaced RDP 16S db by SILVA
- Added classification of all detected and valid 16S sequences in taxonomic classification
- Added a 'debug' option for better on-site/remote debugging
- Updated PubMLST to 2019-10-02
- Updated CARD db to 3.0.5 and RGI to 5.1.0
- Updated VFDB to 2019-10-02
- Discarded unnecessary dependencies from Docker image
- Applied several bugfixes and minor improvements to report pages
- Added a dynamic max cpu/core threshold for 3rd party executables (#2)
- Fixed data table localization
- Fixed scaffold table download file names
- Removed unnecessary dependencies
- Updated source code library versions
- Fixed calculation of contig coverages for hybrid assemblies
- Improved resolution of phyl. trees
- Fixed calculation of PE read mapping metrics
- Fixed GenBank CDS extraction in VF detection
- Changed reports locale to EN
- Applied many bugfixes and minor improvements to report pages
- Fixed and improved cloud orchestration logic
- Fixed allel detection in MLST
- Fixed ABR gene detection and length calculation
- Applied minor improvements and bugfixes to report pages
- Added support for ONT sequencing platform
- Added option to skip comparative analyses
- Simplified Docker based execution
- Removed necessarity of extra cloud images and tarballs
- Updated CARD db
- Updated VF db
- Applied many bugfixes and minor improvements to report pages
##Enhancements
- Updated NCBI tbl2asn
- Fixed VF reports bug introduced by CARD/ResFinder replacement
- Added option to skip comparative analyses
- Applied many bugfixes and minor improvements to report pages
- Replaced ResFinder by CARD as annotation database
- Harmonized variable names in cloud property file
- Fixed NPE in ANI calculation
- Applied many bugfixes and minor improvements
- Applied many bugfixes and minor improvements
- Added support for PacBio Sequel protocol
- Added a virulence factor (VF) detection analyses based on VFDB
- Fixed PacBio analysis workflow
- Fixed internal step selection
- Reviewed QC contamination plots
- Added comprehensive help sections to report pages
- Applied many bugfixes and minor improvements to report pages
- Replaced ResFinder by CARD as annotation database
- Added a 16S rRNA based taxonomic classification
- Added a core/pan genome analysis
- Replaced CONTIGuator by MeDuSa (single -> multi reference based scaffolding)
- Updated annotation databases (Refseq Feb 17)
- Updated annotation databases (RFAM 12.2)
- Updated ABR database (CARD 1.1.8)
- Adjusted SGE CPU/RAM resource requests
- Applied many bugfixes and enhancements to HTML report pages
- Added an antimicrobial resistance detection analysis based on CARD db
- Added a MLST analysis
- Added support for draft reference genomes
- Added ANI computation for references
- Added a length and coverage based contig filter after assembly
- Reorganized and improve all report pages
- Decoupled ASA³P from BCF ressources
- Added ResFinder and VFDB as annotation reference databases
- Provided Prokka with gram +/- information
- Updated annotation databases (RFAM 12.1)
- Provided unique locus tags to contigs during annotation
- Reimplemented cluster scripts
- Annotate SNPs with SnpEff
- Added circular genome plot to annotation report
- Handle failed/skipped steps
- Added interactive JS visualizations
- Several bugfixes and minor improvements
- Added an phylogeny analyses
- Added a reporting stage creating HTML reports