![]() ![]() Thus, here we cannot confidently state that an classification on the family level is more correct than an classification on the order level. This is true for example for the family Dehalococcoidaceae, which in our databases is the sole representative of the order Dehalococcoidales. However, it is not always possible for conflict to arise, because in some cases no other sequences from the clade are present in the database. Since it did not, we can trust the low-level classification. Namely, if there were conflicting classifications, the algorithm would have made the classification more conservative by moving up a level. ![]() When we want to confidently go down to the lowest taxonomic level possible for a classification, an important assumption is that on that level conflict between classifications could have arisen. Marking suggestive taxonomic assignments with an asterisk $ CAT bin -b ĬAT summarise currently does not support classification files wherein some contigs / MAGs have multiple classifications (as contig_2 above). When the download and processing of the files is finished successfully you can build a CAT database with CAT prepare.įor all command line options available see This can come in handy for downstream analyses tools that require a phylogeny to be present to calculate diversity indices based on some metric that takes that information into account. In addition, the newick formatted trees for Bacteria and Archaea are downloaded and - artificially - concatenated under a single root node, to produce an all.tree file.This is also used by CAT prepare for proper LCA identification. The mapping of all protein sequences (duplicates or not) to their respective taxonomy is created.This information is later used by CAT prepare to assign the LCA of the protein sequence appropriately in the. Only one representative sequence is kept, with information on the rest of the accessions identified as duplicates encoded in the fasta header. This is to reduce the redundancy in the DIAMOND database to be created, thus simplifying the alignment process.Įxact duplicate sequences are identified based on a combination of the MD5 sum of the protein sequences and their length. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |