v1.3.0 - massively reduced DB size

This update release provides new features, enhancements and several bugfixes.
Most important change: For the taxonomic species identification Kraken has been replaced by a combined Mash/ANI approach against RefSeq genomes which resulted in a massively reduced db size, making ASA³P even more eligible for smaller systems!

Features

• Replaced Kraken based kmer taxonomic classification by a Mash lookup / ANI computation approach

Updates & Enhancements

• 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

v1.2.2

This is a patch release improving the -c/--check option in order to pre-check the configuration file.
Config checks and error messages have been improved and streamlined.

v1.2.1

This is a patch release fixing a "permission denied" error within the Docker container if an external scratch volume (-s <path>) is not set explicitly.

v1.2.0

This is a new version providing new features, enhancements and bugfixes:

Features

• 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

Updates & Enhancements

• 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

As the ASA³P directory (databases & 3rd party tools) is too big to upload it on GitHub, we provide them on our own servers. Download URLs for all necessary files are given in the readme: https://github.com/oschwengers/asap#availability

v1.1.3

This is a patch release fixing some minor issues and provide some minor enhancements:

• 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

Patch version v1.1.2

This is a patch version providing several minor enhancements and bugfixes:

• 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

As the ASA³P volume containing all databases and 3rd party executables is too big to upload it on GitHub, we provide them on our own servers. Download URLs for all necessary files are given in the readme: https://github.com/oschwengers/asap#availability

Patch version v1.1.1

This is a patch version providing several minor enhancements and bugfixes:

• 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

As the ASA³P volume is too big to upload it on GitHub, we provide them on our own servers. Download URLs for all necessary files are given in the readme: https://github.com/oschwengers/asap#availability

Furthermore, this update also catches up a lacking jump to minor version v1.1.0:

Features

• Added support for ONT sequencing platform
• Added option to skip comparative analyses

Enhancements

• Simplified Docker based execution
• Removed the necessity of extra cloud images and tarballs
• Updated CARD db
• Updated VF db
• Applied many bugfixes and minor improvements to report pages

v1.0.0

The first public version 1.0.0