Releases: ncbi/pgap
2021-07-01.build5508
For real this time. We fixed the issue of missing module 941ff00c0a6010009091__mypyc experienced by several users, by unpinning the schema-salad version (#155).
2021-06-25.build5499
Failed attempt at fixing the issue of missing module 941ff00c0a6010009091__mypyc experienced by several users users, by unpinning the schema-salad version (#155)
2021-05-19.build5429
This release is based on pgap-5.2. It includes the following features and bug fixes:
- Increase in the number of gene symbols should be expected in the annotation of Escherichia coli, Mycobacterium tuberculosis, Acinetobacter pittii, Bacillus subtilis and Campylobacter jejuni genomes. Extra gene symbols are obtained by calculating and mapping orthologs from the reference genome for the species to the annotated genome.
- Switched to CWL v1.2
- Upgraded RFAM to 14.4
- Improved CDS stop finding
- Fixed bugs in the user interface
- Fixed code attempting to extend candidate ORFs beyond the length of the sequence
2021-01-11.build5132
These release is based on pgap-5.0. It includes the following features and bug fixes:
- Improved performance by restricting Blast searches of non-plasmid candidate ORFs and final models to taxonomic-order-specific protein cluster representatives. Models on plasmid sequences continue to be searched against the unrestricted database of protein cluster representatives. As with previous versions, all non-plasmid and plasmid candidate ORFs and final models are searched against the entire collection of BlastRules. No loss in sensitivity or specificity of annotation output was observed with this change.
- Upgraded tRNAscan-SE to 2.0.7
- Fixed CPU resource limits, for all supported container platforms
- Clarified that memory limits are unsupported with Singularity
2020-09-24.build4894
This release is based on pgap-4.13 and stable component SC-24 of NCBI C++ Toolkit. It includes the following features and bug fixes:
- Identifying 16S and 23S rRNA by infernal cmsearch against Rfam SSU and LSU models for bacteria and archaea. This replaces a BLAST-based search against a manually curated NCBI database of ribosomal RNAs.
- Improved annotation of circular sequences with cross-origin CDSs.
- Program changes to correct minor issues and improve performance including tolerance to memory restrictions in BLASTP calculations
- tRNAscan switched to 2.0.6
- CRISPR prediction software switched to v.1.02 made more stable in regards to pilercr failures
2020-07-09.build4716
This release is based on pgap-4.12 and stable component SC-24 of NCBI C++ Toolkit. It includes the following features and bug fixes:
- Program changes to correct minor issues and improve performance
2020-06-10.build4646
This release is based on pgap-4.11. It includes the following features and bug fixes:
2020-03-30.build4489
- Uses pgap 4.11 code base
- Fix bug causing failure in taxcheck when the genome is assigned to the wrong organism
- Extension into gaps fix in genemark
2020-03-16.build4456
Fixed an annotation error that allowed coding regions to have overlapping tRNAs.
2020-02-06.build4373
This release has the following new features:
- Optional taxonomy checking based upon ANI
- Support for containers other than Docker, such as Singularity and Podman
- Self updating for the pgap.py control script
- Numerous minor improvements to the annotation pipeline
- Support for running without accessing the Internet (air-gapped)
- Uses pgap 4.11 code base