Eukaryotic Annotation

Session Leader(s)

• Michael Paulini
• Camilla Santos

Description

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.

Prerequesites

1. Understanding the terms genome assembly, reads, contigs
2. Understanding of linux command line basics

Data

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

Instructions

BRAKER3

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/

create an UCSC assembly hub

time make_hub.py -e my@email.com \
    --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.