LoReAn (Long Read Annotation) for automated eukaryotic genome annotation incorporating long-reads

The LoReAn software is an automated annotation pipeline designed for eukaryotic genome annotation. It is built using previously defined annotation rationale and programs, but the key improvement is the incorporation of single-molecule cDNA sequencing data, such as that produced from Oxford Nanopore and from PacBio. We find this significantly improves automated annotations and reduces the requirements for time-consuming manual annotation.

We are working to improve LoReAn documentation. Meanwhile, some more LoReAn information can be found at bioRxiv (earlier version ) or Plant Physiology (peer reviewed). For those familiar with the annotation process and with docker, there should be enough information to run the program. If you have problems, please open an issue.

This is how LoReAn works: LoReAn schematic view

HOW TO RUN

LoReAn requires three mandatory files:

• Protein Sequences
• Reference genome sequence
• Genome name

To install the software:

Please see the installation instructions for details.

The software can be run after installing by:

lorean -pr protein.fasta -sp spacies genome.fasta 

The full list of options can be found at option instructions or by:

lorean --help

LoReAn can run BRAKER2 to improve Augustus gene prediction;

To do so, short reads from RNA-seq or long reads RNA-seq need to be provided

EXAMPLE DATASET

We made available two datasets that can be used to test LoReAn. The 1st dataset is from Nanopore data of Verticillium dahliae strain JR2 while the second is from PacBio data of Plicaturopsis crispa. Both datasets can be dowloaded from LoReAn Examples

SOFTWARE USED IN THE PIPELINE

• TransDecoder-3.0.1
• samtools v0.1.19-96b5f2294a
• bedtools v2.25.0
• bowtie v1.1.2
• bamtools v2.4.1
• AATpackage r03052011
• iAssembler v1.3.2.x64
• GeneMark-ES/ET v.4.33 64bit (THIS SOFTWARE IS NOT FREE FOR EVERYONE, check installation instruction)
• PASApipeline v2.1.0
• augustus v3.3
• trinityrnaseq v2.5.1
• STAR v2.5.3a
• gmap-gsnap v2017-06-20
• fasta v36.3.8e
• BRAKER v2.0
• EVidenceModeler v1.1.1
• gffread v0.9.9
• genometools v1.5.9

AUTHORS:

• Luigi Faino
• David Cook
• Jose Espejo