Small pipeline combining raw genome-data and VARUS.bam (or RNA-seq data) and run BRAKER3
BRAKER3 from https://github.com/Gaius-Augustus/BRAKER
The best way to use singularity container:
singularity build braker3.sif docker://teambraker/braker3:latest
VARUS from https://github.com/Gaius-Augustus/VARUS
BUSCO from https://busco.ezlab.org/
hisat2 https://github.com/DaehwanKimLab/hisat2
sra-toolkit https://github.com/ncbi/sra-tools requeired version >= 3.0.2
Important: GeneMark-ETP has sra-tools included, but v3.0.1
GeneMark-ETP https://github.com/gatech-genemark/GeneMark-ETP
Input should be a table with at least 1 column:
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
Command line:
varus-braker.py --input table.txt
File config.ini should have pathways to all executables.
[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.
| 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 |
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