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README.TXT
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README.TXT
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% BRAKER2 %
% %
% Authors: Katharina J. Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, %
% Mario Stanke %
% %
% Contact: [email protected] %
% %
% Date: August 22nd 2018 %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1. INTRODUCTION
2. REPOSITORY STRUCTURE
3. INSTALLATION & FURTHER INFORMATION
1. INTRODUCTION
---------------
The rapidly growing number of sequenced genomes requires fully automated methods for accurate gene
structure annotation. With this goal in mind, we have developed BRAKER1 [Hoff et al., 2015], a
combination of GeneMark-ET [Lomsadze et al., 2014] and AUGUSTUS [Stanke et al., 2008, Stanke et al.,
2006], that uses genomic and RNA-Seq data to automatically generate full gene structure annotations
in novel genomes.
However, the quality of RNA-Seq data that is available for annotating a novel genome is variable, and
in some cases, RNA-Seq data is not available, at all. BRAKER2 is an extension of BRAKER1 which
allows for fully automated training of the gene prediction tools GeneMark-EX [Lomsadze et al., 2005,
Ter-Hovhannisyan et al., 2008, Lomsadze et al., 2014] and AUGUSTUS from RNA-Seq and/or protein
homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology
information into the prediction.
In contrast to other available methods that rely on protein homology information, BRAKER2 reaches
high gene prediction accuracy even in the absence of the annotation of very closely related species
and in the absence of RNA-Seq data.
BRAKER2 can also combine RNA-Seq and protein homology information.
2. REPOSITORY STRUCTURE
-----------------------
This repository currently contains three directories:
* BRAKER/scripts/ - all BRAKER source code resides in this folder; it also contains a
subdirectory cfg/ with extrinsic.cfg files for running AUGUSTUS with
different BRAKER-specific input file combinations
* BRAKER/docs/ - contains the userguide as PDF and source files and further subdirectories
with slides and posters from conference presentations of BRAKER
* BRAKER/example/ - contains example data, a subdirectory tests/ with scripts for testing
BRAKER in different modes, and a subdirectory results/ with example
results from the tests.
Note: a large file with RNA-Seq alignments is not hosted on gitub. You
can download that files to the BRAKER/example/ folder from
https://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam (134 MB).
This additional file will be required for executing some of the test
scripts.
3. INSTALLATION & FURTHER INFORMATION
-------------------------------------
Installation instructions and further information on running BRAKER, bug reporting, citing BRAKER
are provided in BRAKER/docs/userguide.pdf.