CAT pack v6.0.1

Notable changes

• Minor release to register for a Zenodo DOI.

CAT pack v6.0

Notable changes

• Change of entry-point for CAT/BAT/RAT: you can now run CAT_pack instead of CAT, for example CAT_pack contigs.
• We welcome a new member to the CAT pack: Read Annotation Tool! RAT uses CAT and BAT annotations as well as direct read mappings to reconstruct accurate taxonomic profiles of metagenomes! To try RAT, run CAT_pack reads.

CAT pack v5.3

Notable changes

• GTDB support.
• Sequence databases (NCBI nr or GTDB) can be downloaded with CAT download, and CAT databases constructed with CAT prepare.
• Sensible defaults of DIAMOND parameters for high memory machines: --top 11 --block_size 12 --index_chunks 1.
• You can now run CAT first, and then run BAT with the predicted proteins fasta and alignment file generated by CAT.
• Preparations for Read Annotation Tool (RAT).

CAT v5.2.3

Notable changes

• Fix for #52.

CAT v5.2.2

Notable changes

• We have added the --no_self_hits flag which suppresses reporting of identical hits by DIAMOND. This is a great option for re-evaluation of sequences that are already present in the nr database.
• Some extra checks and code streamlining.
• Databases generated by CAT prepare now have a slightly different naming scheme: CAT_database.{date} versus {date}.CAT_database in previous versions.

CAT v5.2.1

Notable changes

• Minor bug fix for CAT prepare in the step that checks the available memory.

CAT v5.2

Notable changes

• A big update to the database files: CAT prepare now uses a new mapping file that allows us to assign taxids to up to 20% more proteins than with the previous prot.accession2taxid file. A big shout-out to NCBI for picking up our bug report and combining information from multiple resources into a single mapping file!
• Another update to CAT prepare: file integrity of downloads is assessed based on md5 checksums.
• Change to the output files: the ORF2LCA output file contains a new column for the number of hits the classification is based on.
• Change to the output files: the 'classification' column in the output files previously contained the verdicts classified and unclassified. These two options are now called taxid assigned and no taxid assigned, respectively, in order to prevent confusion about cases where a contig or bin is classified but does not have a classification up to rank superkingdom.
• Change to the output files: while converting to official ranks with CAT add_names, if a classification does not go to lower ranks this is now called no support as opposed to the previous not classified. This should prevent confusion about the meaning of 'classified' even further!

CAT v5.1.2

Notable changes

• Code streamlining.

CAT v5.1.1

Notable changes

• CAT and BAT can now compress the DIAMOND alignment file.
• Import of a gzip compressed alignment file is also supported!

CAT v5.1

Notable changes

• The code has been rewritten to prepare for future extensions.
• We have added the --verbose flag, which will help you crashing bugs in no time!