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Short Description
Long Reads Annotation pipeline
Full Description

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 requirments for time-consuming manual annotation.

We are working to improve LoReAn documentation and getting a paper into bioRxiv. For those familar with the annotation process and with docker, there should be enough infomation to run the program. Otherwise, check back soon ...

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.py <protein.fasta> <genome.fasta> <species name for augustus>

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

lorean.py --help

LoReAn can run BRAKER1 to improve Augustus gene prediction;

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

SOFTWARE USED IN THE PIPELINE

  • samtools v0.1.19-96b5f2294a
  • bedtools v2.25.0
  • bowtie v1.1.2
  • bamtools v2.4.1
  • AATpackage r03052011
  • iAssembler v1.3.2.x64
  • gm_et_linux_64 (THIS SOFTWARE IS NOT FREE FOR EVERYONE)
  • PASApipeline v2.1.0
  • augustus v3.3
  • trinityrnaseq v2.4.0
  • STAR v2.5.2b
  • gmap-gsnap v2017-06-20
  • fasta v36.3.8e
  • BRAKER v1.11
  • EVidenceModeler v1.1.1
  • gffread v0.9.9
  • genometools v1.5.9

AUTHORS:

  • Luigi Faino
  • David Cook
  • Jose Espejo
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lfaino
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