--- name: "ecotag" section: "1" platform: "linux" package: "obitools" version: "1.2.12+dfsg-2" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/ecotag" --- # ecotag(1) description of ecotag ecotag is the tool that assigns sequences to a taxon based on sequence similarity. The program first searches the reference database for the reference sequence(s) (hereafter referred to as ‘primary reference sequence(s)’) showing the highest similarity with the query sequence. Then it looks for all other reference sequences (hereafter referred to as ‘secondary reference sequences’) whose similarity with the primary reference sequence(s) is equal or higher than the similarity between the primary reference and the query sequences. Finally, it assigns the query sequence to the most recent common ancestor of the primary and secondary reference sequences. As input, ecotag requires the sequences to be assigned, a reference database in fasta format, where each sequence is associated with a taxon identified by a unique taxid, and a taxonomy database where taxonomic information is stored for each taxid. ## NAME ecotag - description of ecotag *ecotag* is the tool that assigns sequences to a taxon based on sequence similarity. The program first searches the reference database for the reference sequence(s) (hereafter referred to as ‘primary reference sequence(s)’) showing the highest similarity with the query sequence. Then it looks for all other reference sequences (hereafter referred to as ‘secondary reference sequences’) whose similarity with the primary reference sequence(s) is equal or higher than the similarity between the primary reference and the query sequences. Finally, it assigns the query sequence to the most recent common ancestor of the primary and secondary reference sequences. As input, *ecotag* requires the sequences to be assigned, a reference database in fasta format, where each sequence is associated with a taxon identified by a unique *taxid*, and a taxonomy database where taxonomic information is stored for each *taxid*. *Example:* ``` > ecotag -d embl_r113 -R ReferenceDB.fasta \ --sort=count -m 0.95 -r seq.fasta > seq_tag.fasta ``` The above command specifies that each sequence stored in **seq.fasta** is compared to those in the reference database called **ReferenceDB.fasta** for taxonomic assignment. In the output file **seq\_tag.fasta**, the sequences are sorted from highest to lowest counts. When there is no reference sequence with a similarity equal or higher than 0.95 for a given sequence, no taxonomic information is provided for this sequence in **seq\_tag.fasta**. ## ECOTAG SPECIFIC OPTIONS - **-R \, --ref-database=\** \ is the fasta file containing the reference sequences - **-m FLOAT, --minimum-identity=FLOAT** When the best match with the reference database present an identity level below FLOAT, the taxonomic assignment for the sequence record is not computed. The sequence record is nevertheless included in the output file. FLOAT is included in a \[0,1\] interval. - **--minimum-circle=FLOAT** minimum identity considered for the assignment circle. FLOAT is included in a \[0,1\] interval. - **-x RANK, --explain=RANK** - **-u, --uniq** When this option is specified, the program first dereplicates the sequence records to work on unique sequences only. This option greatly improves the program’s speed, especially for highly redundant datasets. - **--sort=\** The output is sorted based on the values of the relevant attribute. - **-r, --reverse** The output is sorted in reverse order (should be used with the –sort option). (Works even if the –sort option is not set, but could not find on what the output is sorted). - **-E FLOAT, --errors=FLOAT** FLOAT is the fraction of reference sequences that will be ignored when looking for the lowest common ancestor. This option is useful when a non-negligible proportion of reference sequences is expected to be assigned to the wrong taxon, for example because of taxonomic misidentification. FLOAT is included in a \[0,1\] interval. - **-M INTEGER, --min-matches=FLOAT** Define the minimum congruent assignation. If this minimum is reached and the -E option is activated, the lowest common ancestor algorithm tolarated that some sequences do not provide the same taxonomic annotation (see the -E option). - **--cache-size=INTEGER** A cache for computed similarities is maintained by *ecotag*. the default size for this cache is 1,000,000 of scores. This option allows to change the cache size. ## TAXONOMY RELATED OPTIONS - **-d \, --database=\** ecoPCR taxonomy Database name - **-t \, --taxonomy-dump=\** NCBI Taxonomy dump repository name ## OPTIONS TO SPECIFY INPUT FORMAT ### Restrict the analysis to a sub-part of the input file - **--skip \** The N first sequence records of the file are discarded from the analysis and not reported to the output file - **--only \** Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the *–skip* option. ### Sequence annotated format - **--genbank** Input file is in genbank format. - **--embl** Input file is in embl format. ### fasta related format - **--fasta** Input file is in fasta format (including OBITools fasta extensions). ### fastq related format - **--sanger** Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers). - **--solexa** Input file is in fastq format produced by Solexa (Ga IIx) sequencers. ### ecoPCR related format - **--ecopcr** Input file is in ecoPCR format. - **--ecopcrdb** Input is an ecoPCR database. ### Specifying the sequence type - **--nuc** Input file contains nucleic sequences. - **--prot** Input file contains protein sequences. ## OPTIONS TO SPECIFY OUTPUT FORMAT ### Standard output format - **--fasta-output** Output sequences in **OBITools** fasta format - **--fastq-output** Output sequences in Sanger fastq format ### Generating an ecoPCR database - **--ecopcrdb-output=\** Creates an ecoPCR database from sequence records results ### Miscellaneous option - **--uppercase** Print sequences in upper case (default is lower case) ## COMMON OPTIONS - **-h, --help** Shows this help message and exits. - **--DEBUG** Sets logging in debug mode. ## ECOTAG ADDED SEQUENCE ATTRIBUTES - • best\_identity - • best\_match - • family - • family\_name - • genus - • genus\_name - • id\_status - • order - • order\_name - • rank - • scientific\_name - • species - • species\_list - • species\_name - • taxid ## AUTHOR The OBITools Development Team - LECA ## COPYRIGHT 2019 - 2015, OBITool Development Team