README.md

RATT

Rapid Annotation Transfer Tool

SYNOPSIS

RATT_HOME=/path/to/RATT \
ratt \
{-p|--prefix} result-prefix \
{-t|--type} transfer-type \
[{-r|--refseq} reference.fasta] \
reference-annotation-directory query.fasta

DESCRIPTION

ratt (Rapid Annotation Transfer Tool) conducts synteny-based annotation transfer to a given sequence.

ARGUMENTS

REQUIRED

reference-annotation-directory : The directory containing all the reference annotation files to be transferred to the query. These files must be in EMBL format.

query.fasta : The nucleotide sequence to which the reference annotations will be mapped.

-p, --prefix result-prefix : The prefix you wish to give to each result file.

-t, --type transfer-type : The following types can be used:

**Assembly**
:    transfer between different assemblies
**Assembly.Repetitive**
:    As before, but the genome is extremely repetitive.
	 This should only be run if the parameter **Assembly** misses too many annotation tags.
**Strain**
:	 Transfer between strains. Similarity is between 95-99%.
**Strain.Repetitive**
:    As before, but the genome is extremely repetitive.
     This should only be run if the parameter **Strain** misses too many annotation tags.
**Strain.Global**
:    If your assembly doesn't have many gaps and rearrangements, this option might help.
**Species**
:    Transfer between species. Similarity is between 50-94%
**Species.Repetitive**
:    As before, but the genome is extremely repetitive.
     This should only be run if the parameter **Species** misses too many annotation tags.
**Species.Global**
:    As before, but if your assembly doesn't have many gaps and rearrangements, this option might help.
**Multiple**
:    When many annotated strains are used as a reference and you assume that the query genome has many insertions compared to them, this parameter will use the best regions of each reference strain to transfer tags.
**Free**
:    The user sets all **nucmer**(1) parameters individually.
     These parameters must be specified via the following environment variables:

	**RATT_l**
	:    word size
	**RATT_minInd**
	:    identity cutoff
	**RATT_c**
	:    cluster size
	**RATT_g**
	:    max extend cluster
	**RATT_anchor**
	:    anchor choice
	**RATT_rearrange**
	:    rearrange

OPTIONAL

-r, --refseq reference.fasta : Name of multi-fasta file containing the reference sequences corresponding to the EMBL annotation files. IMPORTANT: The fasta sequence header names must exactly match the corresponding EMBL annotation files.

ENVIRONMENT

RATT_HOME : Path to the ratt source directory. This variable must be set for the program to function.

RATT_CONFIG : Path to a custom configuration file to use. As start codons and splice sites might vary between organisms, it will be necessary to generate a configuration file for your specific needs. Example configuration files for bacteria or eukaryotes called RATT.config_bac and RATT.config_euk are provided with the program.

RATT_VERBOSE : If this variable is defined, ratt will report its invocations of external programs.

RATT_DOTRANSLATION : When this variable is set to 1, ratt will include protein amino acid sequences in the output.

SEE ALSO

nucmer(1)

RATT is published as:

Thomas D. Otto, Gary P. Dillon, Wim S. Degrave, Matthew Berriman; RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res 2011; 39 (9): e57. doi: 10.1093/nar/gkq1268