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Liftoff Pipeline Specification

Pipeline Details

  • Name: Liftoff
  • Pipeline UUID: xu5az7hf0xb3wm1he08ezquegzo7z6
  • Version: 1.0.0
  • View Pipeline:

Overview

Liftoff pipeline is designed for mapping annotations between assemblies of the same, or closely-related species. It automates the accurate transfer of gene annotations from a reference genome to a target genome, ensuring reliable mapping while preserving transcript and gene structure.

Key Use cases:

  • Gene Annotation Transfer: Mapping gene annotations from a well-annotated reference genome to a newly assembled genome of the same species.
  • Comparative Genomics: Transferring annotations between closely-related species for comparative analysis.
  • Assembly Updates: Updating gene annotations when moving from an older genome assembly to a newer version.

Features

  • Standalone Tool: No pre-generated "chain" file required - takes genome assemblies and reference annotation as direct input.
  • Minimap2 Integration: Uses Minimap2 for efficient alignment of gene sequences rather than whole genomes.
  • Structure Preservation: Maintains transcript and gene structure while maximizing sequence identity.
  • Conflict Resolution: Automatically detects and resolves overlapping gene mappings by determining most-likely mis-mapped genes.
  • Additional Copy Detection: Identifies additional gene copies in the target assembly not present in the reference annotation.
  • Flexible Parameters: Customizable alignment parameters, coverage thresholds, and sequence identity requirements.
  • Containerized Execution: Runs in Docker container (quay.io/viascientific/liftoff:1.0) for reproducible results.

Input/Output Specification

Inputs

Required

Reference Genome FASTA

  • Description: Reference genome assembly in FASTA format from which annotations will be lifted.
  • Format: .fasta
  • Example File Path: /path/to/reference/genome.fasta

Target Genome FASTA

  • Description: Target genome assembly in FASTA format to which annotations will be mapped.
  • Format: .fasta
  • Example File Path: /path/to/target/genome.fasta

Reference Annotation GTF

  • Description: Reference gene annotation file containing gene structures to be lifted over.
  • Format: .gtf
  • Example File Path: /path/to/reference/annotation.gtf

Optional Inputs

Feature List File

  • Description: Text file specifying particular features to lift over (optional filtering).
  • Format: .txt
  • Example File Path: /path/to/feature_list.txt

Outputs

Reported Outputs

  • Lifted Annotation GTF:
  • Description: Gene annotation file for the target genome with lifted over features
  • Format: .gtf
  • Example File Path: /output/directory/lifted_annotation.gtf
  • Visualization App: IGV, UCSC Genome Browser
  • Location: Output Folder

Associated Processes

References & Additional Documentation

  • Related Papers: Alaina Shumate, Steven L Salzberg, Liftoff: accurate mapping of gene annotations, Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1639–1643, https://doi.org/10.1093/bioinformatics/btaa1016
  • Pipeline Repository: https://github.com/agshumate/Liftoff