Releases · tseemann/prokka (original) (raw)

Heading into the sunset

The future

This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwengers instead - it's a great successor to Prokka without all the technical debt from what was my first real bioinformatics tool. Keep on annotatiing! :-)

Major changes

• Removed all bundles binaries - please use bioconda or environment.yml
• New sprot DBs for bacteria, archaea, viruses
• New HAMAP HMMs for bacteria, archaea
• Support gzip compressed HMMs
• New internal database update system I can use
• Removed support for Homebrew
• Moved TRAIVIS-CI to Github Actions

Pull requests accepted

• Link --proteins section of manual to fasta-db-format section by @0xaf1f in #611
• Prodigal: don't set metagenome mode if training file given by @jvolkening in #538
• Use version objects for version cmp by @kiwiroy in #517
• Speed up overlap lookup in CDS stage by @fluhus in #493

New Contributors

• @0xaf1f made their first contribution in #611
• @jvolkening made their first contribution in #538
• @kiwiroy made their first contribution in #517
• @fluhus made their first contribution in #493

Full Changelog: https://github.com/tseemann/prokka/compare/v1.4.14.5..v1.15.6

Keep on annotating!

v1.14.5

Changes

• massive Rfam 14.1 db update (@standage 👏 )
• complete HAMAP, AMR and sprot db updates (@tseemann)
• support for SignalP 5.0 (@ealdraed)
• new --prodigaltf option to provide Prodigal training file
• fix temp file clashes if same --outdir
• remove legacy --docs command
• fix version checking logic with blast+ 2.10.0
• write GFF parents before children (@ucpete)
• cleanups (@nsoranzo @peterjc)

Still not done

• plasmid and phage protein database
• make tbl2asn optional

Now with AMR and IS/transposase databases

Changes in this version

• add ISFinder database to properly annotate transposase families
• add NCBI AMR database to properly annotate
• new --dbdir option
• new --coverage option
• check sequence names, especially | chars
• ditch bundled perl modules
• fix conda and brew packages
• bug fixes for minced (CRISPR) and COG
• updated binaries including tbl2asn
• static ordering now for terms in the .txt output

Coming soon

• better plasmid protein databases
• update ncRNA database
• ability to disable tbl2asn and Genbank output

The COGs are in motion

Changes

• Updated sprot databases and added COG terms where availabe (WORK IN PROGRESS)
• TSV file now has COG and len_bp columns

Bug fixes

• Fixed faulty TSV file output
• Fixed some wrong exit codes
• prokka --help now goes to stdout, and erroneous help to stderr
• Fixed prokka --docs
• Updated bundled binaries for Linux and macOS including tbl2asn

Docs

• Streamlined documentation, fixed typos
• Clearer install instructions

Infrastructure

• TRAVIS support
• Added test file test/plasmid.dna

Planned for 1.14

• Full COG support
• GO term support
• Revamped primary database engine

Beware the Ides of March

Two years in the making, too many people to list individually, but thank you to everyone!

• Lots of bug fixes.
• Improved documentation, especially installation
• Newer static binaries for Linux and MacOS
• Updated protein and ncRNA databases
• Better default unique locus_tag based on contig MD5
• Option --cdsrnaolap to allow tRNA/rRNA overlapping CDS
• Option --addmrna to add mRNA features for each CDS
• Option --noanno to just predict CDS coordinates but not /product
• Option --fast to just BLAST sprot and ignore slower HMMs
• New .tsv output of annotated features
• Better log file

Valentines Day Edition

Show your contigs how much you love them.

Melbourne Winter Edition

Lots of bug fixes. More flexibility. Better results. Same awesome speed.