varus-braker

Genome Annotation Pipeline using BRAKER3 This repository provides a small but powerful pipeline for automated genome annotation, integrating raw genome data with VARUS (or RNA-seq data) and running the BRAKER3 annotation tool. The pipeline is designed for users who need to annotate multiple species efficiently.

Key Features

Automated Data Retrieval: The pipeline automatically selects suitable RNA-seq data for each species if not provided. The only required input is a simple table listing species and optional links to their corresponding DNA and/or RNA data. BRAKER3 Integration: It seamlessly runs the BRAKER3 annotation tool to produce high-quality genome annotations. High Throughput Compatibility: Built to run on any High-Performance Computing (HPC) system with SLURM as the job scheduler, making it suitable for large-scale genome annotation projects. Getting Started To use this pipeline, provide a table with the list of species, along with optional links to DNA and RNA-seq data. The pipeline will handle the rest, retrieving RNA-seq data if necessary and performing the annotation using BRAKER3.

Included Tools

• BRAKER3: A pipeline for the prediction of protein-coding genes.
• VARUS: A tool for automated RNA-seq data selection.
• BUSCO: Benchmarking Universal Single-Copy Orthologs to assess genome assembly completeness.
• HISAT2: A fast and sensitive alignment program for mapping RNA-seq reads to genomes.
• SRA Toolkit: Tools for working with data in the Sequence Read Archive (v3.0.2 or later).
• GeneMark-ETP: A suite for gene prediction, including support for RNA-seq.

Getting Started

Users need only provide a table with a list of species and optional DNA/RNA data links. The pipeline will automatically retrieve and process the necessary data, running the annotation through BRAKER3.

See table_example.tbl Columns are divided by tab You may use without DNA-link, will try to find genome in ncbi-databse. RNA-files should have "_1" and "_2" parts in names.

SPECIES_NAME DNA_LINK RNA_LINKS[optional,ID1_1,ID1_2,ID2_1,ID2_2 ... ]
Drosophila melanogaster https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz   /home/user/genomes/RNA/SRR13030903_1.fastq,/home/user/genomes/RNA/SRR13030903_2.fastq
Tribolium castaneum     https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/335/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.fna.gz 
Bombyx mori
#You may add commentaries into the table and also use local files, need absolute path
Drosophila Melanogaster /home/user/genomes/Drosophila/genome.fasta.masked
Populus trichocarpa     /home/user/genomes/Populus/genome.fasta.masked
Arabidopsis thaliana
Caenorhabditis elegans

Use Cases

Genome Annotation for Multiple Species Genomics Research and Bioinformatics Studies Installation and Usage For detailed instructions on setting up the environment, configuring the pipeline, and running it on various HPC systems, please refer to the repository's documentation.

Configuration

File config.ini should have pathways to all executables.

[MAIN]
species_info = /home/user/data/list.tbl


[VARUS]
varus_path = /home/user/VARUS
hisat2_path = /home/user/hisat2
sratoolkit_path = /home/user/sratoolkit.3.0.2-ubuntu64/bin
batchsize = 100000
maxbatches = 1000

[BRAKER]
braker_cmd = /home/user/braker3/BRAKER/scripts/braker.pl 
augustus_config_path = /home/user/Augustus/config
augustus_bin_path = /home/user/Augustus/bin
augustus_scripts_path = /home/user/Augustus/scripts
diamond_path = /home/user/
prothint_path = /home/user/ProtHint/bin
genemark_path = /home/user/GeneMark-ETP/bin
orthodb_path = /home/user/orthodb-clades
excluded = species


[SLURM_ARGS]
partition = snowball
cpus_per_task = 36
module_load = module load bedtools

In case using singularity containter :

[VARUS]
varus_path = /home/user/VARUS/
hisat2_path = /home/user/hisat2
sratoolkit_path = /home/user/sratoolkit.3.0.2-ubuntu64/bin
batchsize = 100000
maxbatches = 1000


[BRAKER]
braker_cmd = singularity exec braker.sif braker.pl 
genemark_path = /home/user/GeneMark-ETP/bin
excluded = species

[SLURM_ARGS]
partition = snowball
cpus_per_task = 48
module_load = module load bedtools
    module load singularity

Please choose the optimal batchsize and maxbatches values: huge batchsize could lead to increasing running time.

Accuracies

	Gene		Transcript		Exon
	Sn	Sp	Sn	Sp	Sn	Sp
Caenorhabditis elegans
batchsize = 1500000 maxbatches = 200 Total = 300M	71.65	83.64	54.17	74.62	80.16	94.40
batchsize = 100000 maxbatches = 1000 Total = 100M	66.19	82.86	49.53	74.93	74.30	94.65
batchsize = 75000 maxbatches = 600 Total = 45M	71.54	85.34	54.21	76.23	78.67	94.84
Arabidopsis thaliana
batchsize = 1500000 maxbatches = 200 Total = 300M	82.63	82.86	57.66	77.95	82.44	93.96
batchsize = 100000 maxbatches = 1000 Total = 100M	82.54	82.96	57.58	78.09	82.20	94.01
batchsize = 75000 maxbatches = 600 Total = 45M	82.64	83.08	57.64	78.14	82.12	94.08
Populus trichocarpa
batchsize = 1500000 maxbatches = 200 Total = 300M	77.93	88.46	63.15	80.83	85.48	94.50
batchsize = 100000 maxbatches = 1000 Total = 100M	78.16	88.53	63.29	81.38	85.57	94.69
batchsize = 75000 maxbatches = 600 Total = 45M	78.33	88.62	63.40	81.52	85.59	94.82
Medicago truncatula
batchsize = 1500000 maxbatches = 200 Total = 300M	50.28	72.97	50.28	65.27	77.79	88.07
batchsize = 100000 maxbatches = 1000 Total = 100M	50.53	72.91	50.53	65.26	77.79	88.22
batchsize = 75000 maxbatches = 600 Total = 45M	50.56	72.95	50.56	65.56	77.71	88.46
Parasteatoda tepidariorum
batchsize = 1500000 maxbatches = 200 Total = 300M	49.02	59.55	41.56	53.45	55.76	86.67
batchsize = 100000 maxbatches = 1000 Total = 100M	46.47	59.71	39.07	53.89	51.97	87.24
Danio rerio
batchsize = 1500000 maxbatches = 200 Total = 300M	56.67	69.55	35.42	66.57	66.07	91.98
batchsize = 100000 maxbatches = 1000 Total = 100M	56.79	70.72	35.36	67.76	65.34	92.60
batchsize = 75000 maxbatches = 600 Total = 45M	56.84	71.11	35.30	68.06	65.85	92.73
Drosophila Melanogaster
batchsize = 1500000 maxbatches = 200 Total = 300M	86.45	90.11	60.03	82.61	83.88	95.34
batchsize = 100000 maxbatches = 1000 Total = 100M	86.89	89.85	60.07	81.99	83.47	94.95
batchsize = 75000 maxbatches = 600 Total = 45M	87.85	90.31	61.19	83.11	84.16	95.43
Solanum lycopersicum
batchsize = 1500000 maxbatches = 200 Total = 300M	46.34	47.79	37.54	47.50	83.88	94.52
batchsize = 100000 maxbatches = 1000 Total = 100M	46.23	47.76	37.43	47.42	83.40	94.47