annotate_my_genomes

annotate_my_genomes annotates genome-guided transcriptomes from RNA-Seq data by leveraging long-read PacBio and hybrid sequencing and integrating StringTie assemblies to improve transcript and gene annotation for vertebrate genomes.

Key Features:

• Hybrid Sequencing Integration: Integrates short and long reads, including PacBio long reads, to generate hybrid assembled transcripts for annotation.
• Coding vs. Non-Coding RNA Distinction: Distinguishes coding RNAs and long non-coding RNAs (lncRNAs) using multiple bioinformatic approaches.
• Gene Reconciliation: Integrates existing annotations from GTF files to reconcile new transcriptomic data with prior gene models.
• Novel Gene Identification: Uses homology assignments to identify novel genes and isoforms, demonstrated on complex loci such as the chicken SCO-spondin gene.
• Cross-Species Applicability: Tailored for vertebrate genomes and applicable across a wide range of species and tissue types.
• Implementation: Implemented using Anaconda, Nextflow, and Docker.

Scientific Applications:

• Improved Genome Characterization: Refines genome annotations and facilitates discovery of novel genes and isoforms from transcriptome data.
• Transcriptome Annotation Reconciliation: Reconciles current annotations with new RNA-Seq-derived transcripts using GTF integration and comparative approaches.
• Research Across Species and Tissues: Enables annotation studies across species and tissue types, including vertebrate models such as chicken.

Methodology:

Processes assembled transcripts from hybrid sequencing data; utilizes StringTie for transcript assembly; applies computational approaches to classify coding versus lncRNAs and reconcile transcripts with existing GTF annotations; employs homology assignments for novel gene and isoform identification.