Genome-annotation_step

First of all, retrieve a BRAKER3 singularity container from https://github.com/Gaius-Augustus/BRAKER
  singularity build braker3.sif docker://teambraker/braker3:latest

Then prepare RNAseq data and homologous protein data
1、For RNAseq data, both paired-end FASTQ files and single-end FASTQ file are available. 
In my case, they are paired-end FASTQ files and located in the ./RNAseq_fastq/ directory and named like SRR21XXXXXX_1.fq.gz and SRR21XXXXXX_2.fq.gz.  
Additionally, if you do not have the RNAseq data, You may need to download these files from a sequencing repository like NCBI SRA.

2、For homologous protein data, gather homologous protein data from related species. 
This could involve downloading protein sequences from databases like NCBI or UniProt.Organize these sequences into a FASTA file.

Finally, run the pipeline:
singularity exec -B /data:/data -B $PWD:$PWD braker3.sif braker.pl \
        --genome=soft_masked.genome.fasta \
        --prot_seq=homologous-protein.fasta \
        --rnaseq_sets_ids=SRR21XXXXXX \
        --rnaseq_sets_dir=./RNAseq_fastq/ \
        --species=species_name \
        --AUGUSTUS_ab_initio \
        --gff3 \
        --threads 8 \
        --workingdir=./workdir_name \
        --AUGUSTUS_CONFIG_PATH=Augustus_config_PATH \
        --AUGUSTUS_BIN_PATH=Augustus_PATH \
        --AUGUSTUS_SCRIPTS_PATH=Augustus_scripts_PATH