RATT-with-GFF

RATT-with-GFF enables Rapid Annotation Transfer Tool (RATT) to be used with a GFF as your annotation file.

RATT is a great tool for transferring annotations from one genome to another, but requires the annotations be in EMBL format.

This pipeline is designed to use existing file conversion tools in order to run RATT with GFF annotation files with minimal information loss

This pipeline was designed for use on linux operating systems.

EXTERNAL DEPENDENCIES:

NBISweden/EMBLmyGFF3 (and all prerequisites)

• https://github.com/NBISweden/EMBLmyGFF3

Rapid Annotation Transfer Tool(RATT) (and all prerequisites)

• http://ratt.sourceforge.net/download.html

The European Molecular Biology Open Software Suite (EMBOSS)

• http://emboss.open-bio.org/html/adm/ch01s01.html

Quality Assesment Tools for Genome Assemblies (QUAST)

• http://bioinf.spbau.ru/en/quast

NOTE FOR UGA USERS:

As of 10/31/17, the Sapelo cluster already has all of these dependencies installed except EMBLmyGFF3. You can install EMBLmyGFF3 to your home directory on Sapelo and add the directory to your path. You will also need to add QUAST "/usr/local/apps/quast/4.5/quast.py" to your path.

USAGE:

Requires all files be in the same directory that you are running the script from

./RATTwithGFF.py [reference-GFF] [reference-FASTA] [query-FASTA] [run-ID] [RATT-Transfer-Type]

Argument	Description
reference-GFF:	Genomic GFF containing the annotations you wish to transfer
reference-FASTA:	Genomic FASTA containing the sequences corresponding to the reference-GFF
query-FASTA:	Genomic FASTA that you wish to transfer the annotations to
run-ID:	A name added as a prefix to each RATT result file
RATT-Transfer-Type:	The set of parameters you wish RATT to use when transferring annotations

• valid Transfer-Type options: Assembly, Assembly.Repetitive, Strain, Strain.Repetitive, Species, Species.Repetitive, Multiple
• See for more info on RATT parameters: http://ratt.sourceforge.net/documentation.html

EXAMPLE

./RATTwithGFF.py ref.gff ref.fasta query.fasta refToQuery Strain

OUTPUT:

contig_fasta: contains the reference sequence split into separate fasta files for each contig/chromosome

contig_gff: contains the reference annotations split into seperate gff files for each contig/chromosome

contig_embl: contains the annotations for each reference contig/chromosome as an EMBL file

[run-ID]_RATT: contains the RATT output files organized into subdirectories

• final_embl contains the RATT transferred annotations in EMBL format for each query contig/chromosome
• final_gff contains the RATT transferred annotation in GFF format for each query contig/chromosome as well as a genomic gff
• transferStats.csv comma-delimited file containing the unique feature counts for the reference GFF and newly generated GFF. Also contains statistics related to to the quality of the assembly.