This release is based on PGAP-6.3. It includes the following features and bug fixes:

• Added more stringent filtering of low coverage and complexity protein alignments, resulting in better annotation of long protein models
• Incorporated CheckM (Parks, Donovan H et al. Genome research vol. 25,7 (2015): 1043-55) for calculating the completeness and contamination of the assembly based on the presence/absence of lineage-specific markers in the set of PGAP-predicted models
• Added import traceback #224
• Bug fix: switched to newer docker hub repository version v2
• Bug fix: better handling of the "isolate" FASTA modifier.

Third Party Software Versions Used

No changes since the previous release.

• tRNAScan-SE v.2.0.9
• hmmer v.3.1b2
• CRISPR v.1.02
• AntiFam v.3.0
• Rfam v.14.4
• GeneMarkS-2 v.1.14_1.25
• CheckM v.1.2.1