- Michael Paulini
- Camilla Santos
This is a workshop on eukaryotic gene annotation using BRAKER developed by Katharina Hoff et.al. We will cover alternative tools and cases where manual intervention might be needed.
- Understanding the terms genome assembly, reads, contigs
- Understanding of linux command line basics
in input_data/
- The data chromosome 1 of the ASG Crambe crambe assembly published as GCA_963924555.1 - odCraCram1_SUPER1.fa.masked
- RNASeq is a subsample of mRNA SRA submissions created by VARUS (Bruhn et al. 2019, BMC Bioinformatics, 20:558) - odCraCram1_SUPER1_RNASeq.bam
- a subsampled reference protein set - subsampled_porifera_proteins.fa
run BRAKER3 with proteins + RNASeq
cd /workspace/BGA24
# run BRAKER3
time braker.pl --workingdir=BRAKER3 --genome=input_data/odCraCram1_SUPER1.fa.masked --bam=input_data/odCraCram1_SUPER1_RNASeq.bam \
--prot_seq=input_data/subsampled_porifera_proteins.fa --AUGUSTUS_BIN_PATH=/usr/bin/ \
--AUGUSTUS_SCRIPTS_PATH=/usr/share/augustus/scripts/ --threads 8 \
--busco_lineage=metazoa_odb10 \
--gm_max_intergenic 10000 --skipOptimize # remember to remove both these options for real jobs!
it should take ~30mins with 8 cores. There are precalculated files in example_output/
time make_hub.py -e [email protected] \
--genome /workspace/BGA24/BRAKER/odCraCram1_SUPER1.fa.masked --long_label "Chromosome 1 of the Crambe crambe genome" \
--short_label odCraCra1_1 --bam /workshop/BGA24/BRAKER/VARUS.bam --threads 8 \
--latin_name "Crambe crambe" \
--assembly_version "artifically split custom assembly" \
--hints /workspace/BGA24/BRAKER3/hintsfile.gff \
--gene_track /workspace/BGA24/BRAKER3/braker.gtf BRAKER3
... which currently breaks, due to an incompatible gitpod library. So we will use https://asg_hubs.cog.sanger.ac.uk/assembly_hubs/hub.txt instead.