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Article summary:
1. CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms.
2. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against a protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.
3. CAT and BAT can be run from intermediate steps if files are formated appropriately, or installed via Bioconda.
Article analysis:
The article is written in a clear and concise manner, providing detailed instructions on how to install, use, and interpret the output files from CAT and BAT. The article also provides information on where to find the necessary database files for running CAT and BAT, as well as instructions on how to generate them if needed.
The article is reliable in terms of its content; it provides accurate information about the algorithms used by CAT and BAT, as well as detailed instructions on how to use them. Furthermore, it includes a link to a paper describing the algorithm together with extensive benchmarks which adds credibility to the article's claims.
The article does not appear to have any biases or one-sided reporting; it presents all relevant information in an unbiased manner without making any unsupported claims or omitting important points of consideration. It also does not contain any promotional content or partiality towards either CAT or BAT.
The only potential issue with this article is that it does not mention any possible risks associated with using CAT or BAT; however, since this is an instructional article rather than a research paper this omission is understandable.