BRAKER Container

BRAKER2 is a gene prediction program that uses GeneMark-EXand 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.

Getting Started

To get the container:

singularity pull braker2.sif shub://aseetharam/braker

This will create a braker2.sif image, with braker installed within the image. Before running, copy augustus_config directory as it needs to be writeable:

singularity exec braker2.sif cp -R /usr/local/config augustus_config

Prerequisities

In order to run this container you'll need Singularity installed.

Usage

BRAKER usage can be found by running:

singularity run --no-home --home /opt/gm_key --cleanenv braker2.sif braker.pl --help

Environment Variables

• PATH Location for all the installed tools
• AUGUSTUS_SCRIPTS_PATH misc. scripts used by augusutus
• AUGUSTUS_BIN_PATH augustus binaries
• GENEMARK_PATH GeneMark scripts
• ALIGNMENT_TOOL_PATH alignment programs that braker needs

Example run

For running on your data:

readonly SINGULARITY_IMAGE=/path/to/braker2.sif
readonly BAM=/path/to/rnaseq.bam
readonly GENOME=/path/to/genome-masked.fasta
readonly PROT_SEQ=/path/to/mikado-proteins.faa
readonly SPECIES="unique-name"

# gffread adds `.` for stop codons, replace it with `*`
sed '/^[^>]/s/\./*/' ${PROT_SEQ} > ${PROT_SEQ##*/}.new

singularity pull braker2.sif shub://aseetharam/braker
singularity exec ${SINGULARITY_IMAGE} cp -R /usr/local/config augustus_config

env time -v singularity run \
    --no-home \
    --home /opt/gm_key \
    --cleanenv \
    --env AUGUSTUS_CONFIG_PATH=${PWD}/augustus_config \
    ${SINGULARITY_IMAGE} braker.pl \
        --cores ${SLURM_JOB_CPUS_PER_NODE} \
        --species=${SPECIES} \
        --genome=${GENOME} \
        --bam=${BAM} \
        --prot_seq=${PROT_SEQ##*/}.new \
        --prg=gth \
        --gth2traingenes \
        --gff3

Authors

• Nathan Weeks - Initial work - WebPage
• Arun Seetharam - maintainer - WebPage

See also the list of contributors who participated in this project.