FOFN MOTD 80 80

This is version 1.0.0 but there is nothing that special about it.

• new --fofn option for bulk scanning
• default --mincov 80 and --mincov 80
• new megares database and docs
• warn user when download fails in abricate-get_db
• new ncbi and card database
• add message of the day at end of each file run

Are we there yet?

Databases

• Updated NCBI data source
• Added MEGARES 2.00 database
• Updated NCBI and CARD bundled databases

Bug fixes

• correct CARD coordinates when revcom
• sort ABx names
• correct protein search tool (experimental)
• missed hit when blast used stderr output

Documentation

• explained --summary option better
• newer references and citations
• explained RESISTANCE annotation

Resistance is not futile, it's a new column name

• handle FASTA,Genbank,EMBL and gz,bz2,zip via any2fasta
• updates to all databases
• new STRAND column in output
• new RESISTANCE column in output (for CARD,NCBI,Resfinder --db)
• bug fixes
• major fix for --summary option
• fixed URLs to databases
• fixed parsing issues with databases
• documentation and --help improvements

Moar databaz

• new --threads option
• new ecoli_vf database from PHAC
• updated databases: ncbi, resfinder, card
• cleaner --help output
• remove File::Slurp dependency

Play your CARDs right

Databases:

• update to CARD 2.0
• updated NCBI, Resfinder and VFDB
• remove NCBI-Betalactamase (now part of NCBI)

Features:

• added PRODUCT column
• updated docs
• better --help output

Bug fixes:

• ensured BLAST installed for --setupdb
• proper error codes for --help etc
• --summary honours --csv now

Dev:

• TRAVIS support

Sneaky bugs

• Fixed bodgy --summary option. We can start using it now properly.
• Made --list go to STDOUT and be TSV (or CSV) output so apps can query what --dbs exist.
• Updated docs accordingly

NCBI is in the game

• no longer put blast indices in git, only fasta - need --setupdb before it will work
• new NCBI database: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047
• updated bundled CARD, Resfinder
• add --mincov option to filter on coverage
• remove perlisms from the --help output
• improved documentation
• don't barf on empty db folders

Not just FASTA anymore

• add support for .gbk and other formats
• support .gz compressed data
• updated databases CARD, ARG-ANNOT and Resfinder (including mcr-3)
• Resfinder downloader uses bitbucket instead of redundant download site
• Added --check option
• New dependencies: unzip, gzip, and seqret from EMBOSS

Abricate all the things

• Use 5 inbuilt databases: CARD, Resfinder, ARG-ANNOT, NCBI Betalactamases, VFDB with --db
• Add custom databases, and see them with --list
• Combine multiple reports into a summary with --summary
• Better GAPS column
• New DATABASE and ACCESSION columns

Bug fixes + updated Resfinder inc mcr-1