funannotate v0.3.9

• bug fix to funannotate compare that was not pulling orthology groups for the final annotation table
• added transcription factors to output of all annotation table.

funannotate v0.3.8

• bug fix in funannotate compare that was calculating MEROPS summary stats incorrectly
• added --minlen option to funannotate sort to discard short contigs

funannotate v0.3.7

• move install to the funannotate wrapper, funannotate setup
• fix bug with custom input folders in funannotate annotate
• output proteins/transcript files for both funannotate predict and funannotate annotate

funannotate v0.3.6

• bug fix in funannotate predict when using BUSCO the EVM input was pulling entire gene models instead of sliced models
• bug fix where BUSCO models were within 100 bp of the start or end of contig resulting in a bedtools range slicing error
• remove slicing of hints file for parallel AUGUSTUS method as splitting the hints file was a slow, faster to just pass the entire hints model to each contig chunk and let AUGUSTUS filter it.

funannotate v0.3.5

• update to the way that funannotate predict parses maker2 results, now using maker models directly as opposed to pulling out annotation from each predictor.
• bug fix if running funannotate compare with a single species

funannotate v0.3.4

• fix to the braker1 method where augustus output was not properly found
• minor update to --optimize_augustus training to align with method used in braker1

funannotate v0.3.3

• fix issue with parallel augustus where very large scaffolds would cause large memory usage, script now chunks the data into 500 kb sections with 10 kb overlaps on each side, runs in parallel, and then combines the results.
• re-ordered transcript evidence in funannotate predict to address providing hints to augustus
• some minor bug fixes

funannotate v0.3.2

• build a check for augustus version and test if it will function with busco and braker1
• revamped busco mediated training of augustus to run busco quickly, filter evidence data corresponding to busco models, filter genemark-ES data, run evidence modeler to get high quality gene sets, filter EVM output with busco to build a final augustus training dataset, and finally train augustus
• improved system info reporting
• due to problems with installing augustus on different operating systems, augustus is not installed default via brew install funannotate. However, running funannotate predict without a version of augustus installed will give you some hints on how to install it for your system.

funannotate v0.3.1

• important bug fix for augustus, previous versions were running augustus with the stop codon inside the prediction, which results in the gene models to fail validation in evidence modeler, thus this update is recommended for all users
• added high quality augustus models to be pulled out of annotation if they are represented by evidence using the --hintsfile, these models are passed to EVM with additional weight
• fixed genemark bug where a single contig resulted in an error, thus funanntoate predict can now handle a single contig as input correctly.

funannotate v0.3.0

• improvements to the gene model filtering in funannotate predict, ability to keep gene models without proper stop codons if desired, --keep_no_stops
• augustus is now multi-threaded
• upgrade of packaged BUSCO to v1.2, slightly faster runtime and simplified code
• non-fungal options are now included in funannotate, however use with non fungal genomes has not been extensively tested. Options of note are --organism, --busco_db, --eggnog_db
• secondary metabolism enzymes added to funannotate compare if genomes were annotated with antiSMASH