An introduction to Genome Annotation of non-model organisms

This is the github repo for the the Genome Annotation Workshop The workshop is focused on annotating genomes of non-model organisms using a custom pipeline of multiple tools. In the workshop different strategies, such as homology-based, ab initio, and de novo approaches are implemented, using a combination of short and long reads (Iso-Seq) available on NCBI. As examples, a single chromosome from three different organisms is used as a demonstration.

To install this site locally run the following commands:

Clone the repo and cd into it

git clone [[email protected]:griffithlab/rnabio.org.git](https://github.com/francicco/GenomeAnnotationWorkshop2024.git)

Install the following software and their dependencies:

STAR | Minimap2 | Samtools | Bedtools | Diamond | Miniprot | BRAKER | Cufflinks | BUSCO | compleasm | Stringtie | Scallop | IsoQuant | Trinity | TransDecoder | Portcullis | Mikado | Miniprot2SplicedNucl.py | IsoQuantGTF2BED12v0.1.py | sam2psl.py | Analyze_Diamond_topHit_coverage.R | UniProtDB ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

The workshop is divided into four section

1. RNAseq mapping on the reference genome (Short-reads & Iso-Seq)
2. Homology and evidence-based prediction of protein coding genes (PCGs) using BRAKER2
3. De Novo annotation using Short-reads RNAseq using Trinity
4. Ab Initio annotation using Short-reads RNAseq & Long-reads RNA-Seq
5. Metrics to evaluate annotations, Splice-site filtering, and Annotation Consensus using Mikado

All data is available at this link, but don't forget to set up your environment!!!