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ECOTAG(1) OBITools ECOTAG(1)

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 <FILENAME>, --ref-database=<FILENAME>
<FILENAME> 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=<KEY>
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 <FILENAME>, --database=<FILENAME>
ecoPCR taxonomy Database name

-t <FILENAME>, --taxonomy-dump=<FILENAME>
NCBI Taxonomy dump repository name

OPTIONS TO SPECIFY INPUT FORMAT

Restrict the analysis to a sub-part of the input file

--skip <N>
The N first sequence records of the file are discarded from the analysis and not reported to the output file

--only <N>
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
Input file is in fasta format (including OBITools fasta extensions).

--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
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=<PREFIX_FILENAME>
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
January 28, 2019 1.02 12