annotate_my_genomes – an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing

The advancement of hybrid sequencing technologies is increasingly expanding genome assemblies that are often annotated using hybrid sequencing transcriptomics, leading to improved genome characterization and the identification of novel genes and isoforms in a wide variety of organisms.

Researchers at the Catholic University of the Most Holy Conception, Chile have developed an easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format. The researchers demonstrated the efficiency of this approach by correctly assembling and annotating all exons from the chicken SCO-spondin gene (containing more than 105 exons), including the identification of missing genes in the chicken reference annotations by homology assignments.

PacBio and Illumina reads are aligned to a given reference genome, then the alignments were merged and assembled into isoforms by StringTie. By combined homology identification and coding/noncoding RNA classification, we annotated the resulting GTF file, identifying previously annotated genes (i.e., USCS/NCBI) and missing genes, respectively 

This method helps to improve the current transcriptome annotation of the chicken brain. The pipeline, implemented on Anaconda/Nextflow and Docker is an easy-to-use package that can be applied to a broad range of species, tissues, and research areas helping to improve and reconcile current annotations.

Availability – The code and datasets are publicly available at https://github.com/cfarkas/annotate_my_genomes.